#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_Mutation_Status	i_NTotCov	i_NVarCov	i_NVarRat	i_ORegAnno_bin	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	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
SFPQ	6421	hgsc.bcm.edu	37	1	35658418	35658432	+	In_Frame_Del	DEL	GGTGGCTGCTGCGGT	GGTGGCTGCTGCGGT	-			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	GGTGGCTGCTGCGGT	GGTGGCTGCTGCGGT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr1:35658418_35658432delGGTGGCTGCTGCGGT	ENST00000357214.5	-	1	317_331	c.219_233delACCGCAGCAGCCACC	c.(217-234)ccaccgcagcagccaccg>ccg	p.73_78PPQQPP>P		NM_005066.2	NP_005057.1	P23246	SFPQ_HUMAN	splicing factor proline/glutamine-rich	73	Gln/Glu/Pro-rich.				alternative mRNA splicing, via spliceosome (GO:0000380)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|histone H3 deacetylation (GO:0070932)|mRNA processing (GO:0006397)|negative regulation of circadian rhythm (GO:0042754)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902177)|regulation of circadian rhythm (GO:0042752)|rhythmic process (GO:0048511)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|paraspeckles (GO:0042382)	core promoter binding (GO:0001047)|histone deacetylase binding (GO:0042826)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|transcription regulatory region DNA binding (GO:0044212)|transcription regulatory region sequence-specific DNA binding (GO:0000976)		SFPQ/TFE3(6)	NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(10)|lung(4)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	25		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.196)				ctgctgcggcggtggctgctgcggtggtggcTGTT	0.707			T	TFE3	papillary renal cell																																p.74_78del		Atlas-Indel	.		Dom	yes		1	1p34.3	6421	splicing factor proline/glutamine rich(polypyrimidine tract binding protein associated)		E	.	SFPQ	51	.	0			c.220_234del						PASS	.			136,3204		29,78,1563						1.2	0.0			4	216,6642		53,110,3266	no	coding	SFPQ	NM_005066.2		82,188,4829	A1A1,A1R,RR		3.1496,4.0719,3.4517				352,9846				SO:0001651	inframe_deletion	6421	exon1			.	X70944	CCDS388.1	1p34.3	2014-06-13	2010-05-04		ENSG00000116560	ENSG00000116560		"""RNA binding motif (RRM) containing"""	10774	protein-coding gene	gene with protein product	"""polypyrimidine tract binding protein associated"", ""protein phosphatase 1, regulatory subunit 140"""	605199	"""splicing factor proline/glutamine rich (polypyrimidine tract-binding protein-associated)"""			8449401	Standard	NM_005066		Approved	PSF, PPP1R140	uc001bys.3	P23246	OTTHUMG00000004157	ENST00000357214.5:c.219_233delACCGCAGCAGCCACC	1.37:g.35658418_35658432delGGTGGCTGCTGCGGT	ENSP00000349748:p.Pro78_Pro82del	Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	29	13	0.448276	NM_005066	P30808|Q5SZ71	In_Frame_Del	DEL	ENST00000357214.5	37	CCDS388.1																																																																																			.	.	none		0.707	SFPQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011984.4	NM_005066	
B2M	567	hgsc.bcm.edu	37	15	45007689	45007690	+	Frame_Shift_Del	DEL	TA	TA	-			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	TA	TA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr15:45007689_45007690delTA	ENST00000558401.1	+	2	206_207	c.136_137delTA	c.(136-138)tatfs	p.Y46fs	B2M_ENST00000559220.1_Intron|B2M_ENST00000544417.1_Frame_Shift_Del_p.Y46fs|B2M_ENST00000559916.1_Frame_Shift_Del_p.Y46fs	NM_004048.2	NP_004039.1	P61769	B2MG_HUMAN	beta-2-microglobulin	46	Ig-like C1-type.				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 exogenous protein antigen via MHC class Ib, TAP-dependent (GO:0002481)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|innate immune response (GO:0045087)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|protein refolding (GO:0042026)|regulation of defense response to virus by virus (GO:0050690)|regulation of immune response (GO:0050776)|response to cadmium ion (GO:0046686)|response to drug (GO:0042493)|response to molecule of bacterial origin (GO:0002237)|retina homeostasis (GO:0001895)|T cell differentiation in thymus (GO:0033077)|viral process (GO:0016032)	cytoplasm (GO:0005737)|early endosome lumen (GO:0031905)|early endosome membrane (GO:0031901)|endoplasmic reticulum lumen (GO:0005788)|ER to Golgi transport vesicle membrane (GO:0012507)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)			breast(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(30)|kidney(8)|large_intestine(6)|lung(6)|ovary(2)|skin(2)|urinary_tract(1)	59		all_cancers(109;1.88e-13)|all_epithelial(112;2.13e-11)|Lung NSC(122;2.22e-07)|all_lung(180;1.81e-06)|Melanoma(134;0.0122)		all cancers(107;4.16e-21)|GBM - Glioblastoma multiforme(94;8.97e-07)|COAD - Colon adenocarcinoma(120;0.0357)|Colorectal(105;0.0377)|Lung(196;0.0903)|LUSC - Lung squamous cell carcinoma(244;0.192)		CCTGAATTGCTATGTGTCTGGG	0.401																																					p.45_46del		Pindel,Atlas-Indel	.											B2M,NS,lymphoid_neoplasm,+2,1	B2M	99	1	0			c.135_136del						PASS	.																																			SO:0001589	frameshift_variant	567	exon2			.	AB021288	CCDS10113.1	15q21-q22.2	2013-01-11			ENSG00000166710	ENSG00000166710		"""Immunoglobulin superfamily / C1-set domain containing"""	914	protein-coding gene	gene with protein product		109700					Standard	NM_004048		Approved		uc001zuc.3	P61769	OTTHUMG00000131247	ENST00000558401.1:c.136_137delTA	15.37:g.45007689_45007690delTA	ENSP00000452780:p.Tyr46fs	Somatic	94	.	.		WXS	Illumina HiSeq	Phase_I	76	35	0.461	NM_004048	P01884|Q540F8|Q6IAT8|Q9UCK0|Q9UD48|Q9UDF4	Frame_Shift_Del	DEL	ENST00000558401.1	37	CCDS10113.1																																																																																			.	.	none		0.401	B2M-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254007.2	NM_004048	
CIITA	4261	hgsc.bcm.edu	37	16	11001270	11001271	+	Frame_Shift_Del	DEL	TA	TA	-			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	TA	TA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr16:11001270_11001271delTA	ENST00000324288.8	+	11	2054_2055	c.1921_1922delTA	c.(1921-1923)tatfs	p.Y641fs	CIITA_ENST00000537380.1_Intron|CIITA_ENST00000381835.5_Intron	NM_000246.3	NP_000237	P33076	C2TA_HUMAN	class II, major histocompatibility complex, transactivator	641	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				aging (GO:0007568)|cellular response to electrical stimulus (GO:0071257)|cellular response to exogenous dsRNA (GO:0071360)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|inflammatory response (GO:0006954)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of collagen biosynthetic process (GO:0032966)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of MHC class I biosynthetic process (GO:0045345)|positive regulation of MHC class II biosynthetic process (GO:0045348)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|response to antibiotic (GO:0046677)|response to interferon-gamma (GO:0034341)|transcription, DNA-templated (GO:0006351)	cell surface (GO:0009986)|nucleoplasm (GO:0005654)|PML body (GO:0016605)	activating transcription factor binding (GO:0033613)|ATP binding (GO:0005524)|GTP binding (GO:0005525)|kinase activity (GO:0016301)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)|transferase activity, transferring acyl groups (GO:0016746)			central_nervous_system(1)|large_intestine(7)|ovary(1)|skin(1)|stomach(2)	12						CACGGGACTCTATGTCGGCCTG	0.688			T	"""FLJ27352, CD274, CD273, RALGDS, RUNDC2A, C16orf75, BCL6"""	"""PMBL, Hodgkin Lymphona, """																																p.640_641del		Atlas-Indel	.		Dom	yes		16	16p13	4261	"""class II, major histocompatibility complex, transactivator"""		L	.	CIITA	92	.	0			c.1920_1921del						PASS	.																																			SO:0001589	frameshift_variant	4261	exon11			.	U18259	CCDS10544.1, CCDS66943.1, CCDS73826.1	16p13	2014-09-17	2005-08-12	2005-08-12	ENSG00000179583	ENSG00000179583		"""Nucleotide-binding domain and leucine rich repeat containing"""	7067	protein-coding gene	gene with protein product	"""NLR family, acid domain containing"", ""nucleotide-binding oligomerization domain, leucine rich repeat and acid domain containing"""	600005	"""MHC class II transactivator"""	MHC2TA		8402893	Standard	NM_000246		Approved	C2TA, NLRA	uc002dai.4	P33076	OTTHUMG00000129753	ENST00000324288.8:c.1921_1922delTA	16.37:g.11001270_11001271delTA	ENSP00000316328:p.Tyr641fs	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	97	19	0.195876	NM_000246	A0N0N9|D3DUG0|E9PFE0|Q29675|Q8SNB8|Q96KL4	Frame_Shift_Del	DEL	ENST00000324288.8	37	CCDS10544.1																																																																																			.	.	none		0.688	CIITA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251966.2	NM_000246	
ICE1	23379	hgsc.bcm.edu	37	5	5461621	5461621	+	Frame_Shift_Del	DEL	A	A	-			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr5:5461621delA	ENST00000296564.7	+	13	2396	c.2174delA	c.(2173-2175)tatfs	p.Y725fs		NM_015325.2	NP_056140.1	Q9Y2F5	ICE1_HUMAN		725					positive regulation of intracellular protein transport (GO:0090316)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|snRNA transcription from RNA polymerase II promoter (GO:0042795)|snRNA transcription from RNA polymerase III promoter (GO:0042796)	Cajal body (GO:0015030)|histone locus body (GO:0035363)|transcription elongation factor complex (GO:0008023)|transcriptionally active chromatin (GO:0035327)	protein homodimerization activity (GO:0042803)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(14)|ovary(1)|prostate(4)|upper_aerodigestive_tract(1)	35						GGGATAGAATATACAAAAGTA	0.383																																					p.Y725fs		Pindel,Atlas-Indel	.											KIAA0947_ENST00000296564,NS,carcinoma,-1,2	KIAA0947	301	2	0			c.2173delT						PASS	.						54.0	52.0	52.0					5																	5461621		1850	4094	5944	SO:0001589	frameshift_variant	23379	exon13			.																												ENST00000296564.7:c.2174delA	5.37:g.5461621delA	ENSP00000296564:p.Tyr725fs	Somatic	173	.	.		WXS	Illumina HiSeq	Phase_I	158	30	0.190	NM_015325	Q68DE1|Q6ZT40|Q7L587|Q7Z3A9|Q9NTH9	Frame_Shift_Del	DEL	ENST00000296564.7	37	CCDS47187.1																																																																																			.	.	none		0.383	KIAA0947-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365575.1		
PRDM1	639	hgsc.bcm.edu	37	6	106552891	106552892	+	Frame_Shift_Ins	INS	-	-	GT	rs17066588	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr6:106552891_106552892insGT	ENST00000369096.4	+	5	1090_1091	c.856_857insGT	c.(856-858)cgtfs	p.R286fs	PRDM1_ENST00000369089.3_Frame_Shift_Ins_p.R152fs|PRDM1_ENST00000369091.2_Frame_Shift_Ins_p.R250fs	NM_001198.3	NP_001189.2	O75626	PRDM1_HUMAN	PR domain containing 1, with ZNF domain	286					cell fate commitment (GO:0045165)|eye photoreceptor cell development (GO:0042462)|germ cell development (GO:0007281)|intestinal epithelial cell development (GO:0060576)|maternal placenta development (GO:0001893)|negative regulation of B cell proliferation (GO:0030889)|negative regulation of lipopolysaccharide-mediated signaling pathway (GO:0031665)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of B cell differentiation (GO:0045579)|positive regulation of gene expression (GO:0010628)|post-embryonic development (GO:0009791)|transcription, DNA-templated (GO:0006351)|trophoblast giant cell differentiation (GO:0060707)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(59)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|skin(5)|urinary_tract(2)	94	Breast(9;0.022)	all_cancers(87;2.2e-31)|all_epithelial(87;2.03e-21)|Acute lymphoblastic leukemia(125;4.99e-11)|all_lung(197;7.55e-09)|all_hematologic(75;5.82e-08)|Lung NSC(302;1.28e-06)|Colorectal(196;0.0112)|Ovarian(999;0.0365)		all cancers(137;1.83e-46)|Epithelial(106;5.59e-35)|OV - Ovarian serous cystadenocarcinoma(136;1.99e-20)|GBM - Glioblastoma multiforme(226;3.72e-11)|BRCA - Breast invasive adenocarcinoma(108;1.38e-05)		CTTTAGAAGACGTGGGAGCCCC	0.525			"""D, N, Mis, F, S"""		DLBCL																																p.R286fs		Pindel,Atlas-Indel	.		Rec	yes		6	6q21	639	"""PR domain containing 1, with ZNF domain"""		L	PRDM1,colon,carcinoma,0,1	PRDM1	195	1	0			c.856_857insGT						PASS	.																																			SO:0001589	frameshift_variant	639	exon5			.		CCDS5054.2, CCDS34505.1	6q21	2013-01-08			ENSG00000057657	ENSG00000057657		"""Zinc fingers, C2H2-type"""	9346	protein-coding gene	gene with protein product		603423		BLIMP1		1851123	Standard	NM_001198		Approved	PRDI-BF1	uc003prd.2	O75626	OTTHUMG00000015299	ENST00000369096.4:c.857_858dupGT	6.37:g.106552892_106552893dupGT	ENSP00000358092:p.Arg286fs	Somatic	152	.	.		WXS	Illumina HiSeq	Phase_I	78	19	0.244	NM_001198	B2REA6|E1P5E0|Q86WM7	Frame_Shift_Ins	INS	ENST00000369096.4	37	CCDS5054.2																																																																																			.	.	none		0.525	PRDM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041661.3		
DGKB	1607	hgsc.bcm.edu	37	7	14775822	14775822	+	Intron	DEL	G	G	-	rs370443019|rs66786499|rs139628753	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr7:14775822delG	ENST00000403951.2	-	5	588				DGKB_ENST00000406247.3_Intron|DGKB_ENST00000258767.5_Intron|DGKB_ENST00000403963.1_Intron|DGKB_ENST00000444700.2_Intron|DGKB_ENST00000399322.3_Intron|DGKB_ENST00000402815.1_Intron|DGKB_ENST00000407950.1_Intron			Q9Y6T7	DGKB_HUMAN	diacylglycerol kinase, beta 90kDa						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)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|diacylglycerol kinase activity (GO:0004143)|NAD+ kinase activity (GO:0003951)	p.?(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|liver(1)|lung(34)|ovary(4)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	72						TCTATTGTCTGGAAAAAAAAA	0.328													?|GG|G|unsure	2796	0.558307	0.239	0.5432	5008	,	,		17163	0.5655		0.831	False		,,,				2504	0.7127				.		Atlas-Indel	.											.	DGKB	166	.	1	Unknown(1)	stomach(1)	c.169-2C>-						PASS	.		,	1129,2347		197,735,806	25.0	13.0	16.0		,	5.9	1.0	7	dbSNP_134	32	6344,1464		2573,1198,133	no	intron,intron	DGKB	NM_145695.2,NM_004080.2	,	2770,1933,939	A1A1,A1R,RR		18.75,32.4799,33.7735	,	,	14775822	7473,3811	1786	4015	5801	SO:0001627	intron_variant	1607	exon5			.	AB018261	CCDS47547.1, CCDS47548.1	7p21.2	2013-01-10	2002-08-29		ENSG00000136267	ENSG00000136267	2.7.1.107	"""EF-hand domain containing"""	2850	protein-coding gene	gene with protein product		604070	"""diacylglycerol kinase, beta (90kD)"""	DAGK2		7689223	Standard	NM_004080		Approved	KIAA0718, DGK, DGK-BETA	uc003ssz.3	Q9Y6T7	OTTHUMG00000152477	ENST00000403951.2:c.169-3C>-	7.37:g.14775822delG		Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	199	146	0.733668	NM_004080	A4D116|A4D117|A8MXU2|O75241|Q2M377|Q75MF9|Q75MU7|Q86UI5|Q86UM9|Q9UQ29	Splice_Site	DEL	ENST00000403951.2	37	CCDS47547.1																																																																																			G|0.405;-|0.595	0.595	strong		0.328	DGKB-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000326356.2	NM_004080	
SDF2	6388	hgsc.bcm.edu	37	17	26976184	26976185	+	Frame_Shift_Del	DEL	AG	AG	-			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr17:26976184_26976185delAG	ENST00000247020.4	-	3	756_757	c.458_459delCT	c.(457-459)tctfs	p.S154fs	SDF2_ENST00000592250.1_5'UTR	NM_006923.3	NP_008854.2	Q99470	SDF2_HUMAN	stromal cell-derived factor 2	154	MIR 3. {ECO:0000255|PROSITE- ProRule:PRU00131}.				protein glycosylation (GO:0006486)|protein O-linked mannosylation (GO:0035269)	extracellular space (GO:0005615)|membrane (GO:0016020)	dolichyl-phosphate-mannose-protein mannosyltransferase activity (GO:0004169)			endometrium(1)|large_intestine(2)|lung(2)|prostate(2)	7	Lung NSC(42;0.00431)					CCTCAGTGGAAGAGTGTTTGAA	0.505																																					p.153_154del		Pindel	.											.	SDF2	17	.	0			c.459_460del						PASS	.																																			SO:0001589	frameshift_variant	6388	exon3			.	BC001406	CCDS11238.1	17q11.2	2004-02-16			ENSG00000132581	ENSG00000132581			10675	protein-coding gene	gene with protein product		602934				8918255	Standard	NR_045585		Approved		uc002hbw.3	Q99470	OTTHUMG00000132681	ENST00000247020.4:c.458_459delCT	17.37:g.26976186_26976187delAG	ENSP00000247020:p.Ser154fs	Somatic	84	.	.		WXS	Illumina HiSeq	Phase_I	89	21	0.236	NM_006923	Q9BQ79	Frame_Shift_Del	DEL	ENST00000247020.4	37	CCDS11238.1																																																																																			.	.	none		0.505	SDF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255965.2	NM_006923	
NRXN2	9379	hgsc.bcm.edu	37	11	64457918	64457919	+	Frame_Shift_Ins	INS	-	-	C			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr11:64457918_64457919insC	ENST00000377551.1	-	4	1019_1020	c.808_809insG	c.(808-810)gccfs	p.A270fs	NRXN2_ENST00000409571.1_Frame_Shift_Ins_p.A270fs|NRXN2_ENST00000377559.3_Intron|NRXN2_ENST00000265459.6_Frame_Shift_Ins_p.A270fs			Q9P2S2	NRX2A_HUMAN	neurexin 2	270					adult behavior (GO:0030534)|gephyrin clustering (GO:0097116)|neuroligin clustering (GO:0097118)|neuron cell-cell adhesion (GO:0007158)|neurotransmitter secretion (GO:0007269)|postsynaptic density protein 95 clustering (GO:0097119)|postsynaptic membrane assembly (GO:0097104)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|vocal learning (GO:0042297)|vocalization behavior (GO:0071625)	integral component of membrane (GO:0016021)	calcium channel regulator activity (GO:0005246)|cell adhesion molecule binding (GO:0050839)|metal ion binding (GO:0046872)|neuroligin family protein binding (GO:0097109)	p.A270fs*27(1)		breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|liver(1)|lung(34)|ovary(6)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(6)|urinary_tract(1)	71						TCCTCTCCCGGCCCCCCCCTCG	0.634																																					p.A270fs		Pindel	.											NRXN2,colon,carcinoma,+1,1	NRXN2	247	1	1	Insertion - Frameshift(1)	central_nervous_system(1)	c.809_810insG						PASS	.		,	56,4208		0,56,2076					,	4.6	1.0			37	73,8181		0,73,4054	no	intron,frameshift	NRXN2	NM_138732.2,NM_015080.3	,	0,129,6130	A1A1,A1R,RR		0.8844,1.3133,1.0305	,	,		129,12389				SO:0001589	frameshift_variant	9379	exon5			.		CCDS8077.1, CCDS31597.1, CCDS8078.1	11q13	2008-07-18			ENSG00000110076	ENSG00000110076			8009	protein-coding gene	gene with protein product	"""neurexin II"""	600566				1621094	Standard	NM_015080		Approved		uc021qkw.1	P58401	OTTHUMG00000045214	ENST00000377551.1:c.809dupG	11.37:g.64457926_64457926dupC	ENSP00000366774:p.Ala270fs	Somatic	46	.	.		WXS	Illumina HiSeq	Phase_I	54	12	0.222	NM_015080	A7E2C1|Q9Y2D6	Frame_Shift_Ins	INS	ENST00000377551.1	37	CCDS8077.1																																																																																			.	.	none		0.634	NRXN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000104967.3	NM_015080	
FRMPD2	143162	hgsc.bcm.edu	37	10	49409419	49409420	+	Frame_Shift_Ins	INS	-	-	T	rs199957001		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr10:49409419_49409420insT	ENST00000374201.3	-	15	2107_2108	c.1805_1806insA	c.(1804-1806)aagfs	p.K602fs	FRMPD2_ENST00000407470.4_Frame_Shift_Ins_p.K570fs|FRMPD2_ENST00000305531.3_Frame_Shift_Ins_p.K577fs	NM_001018071.3|NM_001042512.2	NP_001018081|NP_001035977.2	Q68DX3	FRPD2_HUMAN	FERM and PDZ domain containing 2	602	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				tight junction assembly (GO:0070830)	basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|tight junction (GO:0005923)	1-phosphatidylinositol binding (GO:0005545)			NS(2)|autonomic_ganglia(2)|breast(5)|cervix(1)|endometrium(3)|kidney(7)|large_intestine(15)|lung(24)|ovary(2)|prostate(1)|skin(3)|urinary_tract(1)	66				Kidney(211;0.201)		TGATGGTGAACTTTTTTTGCTG	0.465																																					p.K602fs		Pindel	.											.	FRMPD2	157	.	0			c.1806_1807insA						PASS	.																																			SO:0001589	frameshift_variant	143162	exon15			.	AK123038	CCDS31195.1	10q11	2010-10-13			ENSG00000170324	ENSG00000170324			28572	protein-coding gene	gene with protein product		613323	"""PDZ domain containing 5C"""	PDZD5C, PDZK5C			Standard	NM_001018071		Approved	MGC35285	uc001jdv.3	Q68DX3	OTTHUMG00000018171	ENST00000374201.3:c.1806dupA	10.37:g.49409426_49409426dupT	ENSP00000363317:p.Lys602fs	Somatic	121	.	.		WXS	Illumina HiSeq	Phase_I	125	28	0.224	NM_001018071	B7WNW0|B7ZML5|Q2VY07|Q6GMQ9|Q6ZN38|Q6ZWI2|Q8N5T9	Frame_Shift_Ins	INS	ENST00000374201.3	37	CCDS31195.1																																																																																			.	.	none		0.465	FRMPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047923.3	NM_152428	
PEAR1	375033	hgsc.bcm.edu	37	1	156877797	156877797	+	Silent	SNP	C	C	A	rs77235035	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr1:156877797C>A	ENST00000338302.3	+	9	1081	c.856C>A	c.(856-858)Cga>Aga	p.R286R	PEAR1_ENST00000292357.7_Silent_p.R286R			Q5VY43	PEAR1_HUMAN	platelet endothelial aggregation receptor 1	286	EGF-like 3. {ECO:0000255|PROSITE- ProRule:PRU00076}.				recognition of apoptotic cell (GO:0043654)	integral component of membrane (GO:0016021)|phagocytic cup (GO:0001891)				breast(1)|central_nervous_system(2)|endometrium(4)|large_intestine(6)|lung(22)|ovary(4)|skin(3)|upper_aerodigestive_tract(1)	43	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)					CCTCTGTGACCGATTCACTGG	0.692													C|||	1140	0.227636	0.2383	0.1931	5008	,	,		12560	0.3502		0.1223	False		,,,				2504	0.2198				p.R286R		Atlas-SNP	.											PEAR1,NS,carcinoma,0,2	PEAR1	118	2	0			c.C856A						scavenged	.	C		972,3404		115,742,1331	13.0	14.0	14.0		856	3.6	1.0	1	dbSNP_131	14	1050,7512		71,908,3302	no	coding-synonymous	PEAR1	NM_001080471.1		186,1650,4633	AA,AC,CC		12.2635,22.2121,15.6284		286/1038	156877797	2022,10916	2188	4281	6469	SO:0001819	synonymous_variant	375033	exon8			TGTGACCGATTCA	AK098809	CCDS30892.1	1q23.1	2008-02-05	2007-10-25	2007-10-25	ENSG00000187800	ENSG00000187800			33631	protein-coding gene	gene with protein product		610278	"""multiple EGF-like-domains 12"""	MEGF12		15851471	Standard	NM_001080471		Approved	JEDI, FLJ00193	uc001fqj.1	Q5VY43	OTTHUMG00000041293	ENST00000338302.3:c.856C>A	1.37:g.156877797C>A		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	227	8	0.0352423	NM_001080471	Q8TEK2	Silent	SNP	ENST00000338302.3	37	CCDS30892.1																																																																																			C|0.810;A|0.190	0.190	strong		0.692	PEAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098937.2	NM_001080471	
TAS2R43	259289	hgsc.bcm.edu	37	12	11244194	11244194	+	Missense_Mutation	SNP	T	T	C	rs71443637	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr12:11244194T>C	ENST00000531678.1	-	1	718	c.635A>G	c.(634-636)cAt>cGt	p.H212R	PRR4_ENST00000536668.1_Intron|TAS2R14_ENST00000381852.4_Intron	NM_176884.2	NP_795365.2	P59537	T2R43_HUMAN	taste receptor, type 2, member 43	212				H -> R (in Ref. 1; AAM19328, 3; AAU21145 and 5; AAI17424). {ECO:0000305}.	detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|G-protein coupled receptor signaling pathway (GO:0007186)	integral component of membrane (GO:0016021)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)|taste receptor activity (GO:0008527)			endometrium(1)|ovary(1)|prostate(2)|urinary_tract(1)	5			OV - Ovarian serous cystadenocarcinoma(49;0.0344)	BRCA - Breast invasive adenocarcinoma(232;0.196)		TCCTTTACCATGGAGCTGCAT	0.408													.|||	3114	0.621805	0.0998	0.7104	5008	,	,		13446	0.9425		0.7525	False		,,,				2504	0.7996				p.H212R		Atlas-SNP	.											TAS2R43,NS,carcinoma,0,2	TAS2R43	19	2	0			c.A635G						PASS	.						123.0	99.0	107.0					12																	11244194		2155	4165	6320	SO:0001583	missense	259289	exon1			TTACCATGGAGCT	AF494237	CCDS53749.1	12p13.2	2012-08-22				ENSG00000255374		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	18875	protein-coding gene	gene with protein product		612668				12379855	Standard	NM_176884		Approved	T2R52	uc001qzq.1	P59537		ENST00000531678.1:c.635A>G	12.37:g.11244194T>C	ENSP00000431719:p.His212Arg	Somatic	21	0	0		WXS	Illumina HiSeq	Phase_I	27	10	0.37037	NM_176884	P59546|Q645X4	Missense_Mutation	SNP	ENST00000531678.1	37	CCDS53749.1	949	0.43452380952380953	28	0.056910569105691054	163	0.45027624309392267	439	0.7674825174825175	319	0.420844327176781	-	2.129	-0.399500	0.04865	.	.	ENSG00000255374	ENST00000531678	T	0.00737	5.76	1.45	-1.32	0.09201	.	.	.	.	.	T	0.00012	0.0000	M	0.86178	2.8	0.80722	P	0.0	.	.	.	.	.	.	T	0.07028	-1.0794	6	0.52906	T	0.07	.	4.3248	0.11034	0.0:0.4339:0.0:0.5661	.	.	.	.	R	212	ENSP00000431719:H212R	ENSP00000431719:H212R	H	-	2	0	TAS2R43	11135461	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.381000	0.07417	-0.374000	0.07967	-1.273000	0.01405	CAT	T|0.599;C|0.401	0.401	strong		0.408	TAS2R43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383561.1	NM_176884	
MST1L	11223	hgsc.bcm.edu	37	1	17083872	17083872	+	RNA	SNP	G	G	A	rs61635893		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr1:17083872G>A	ENST00000455405.2	-	0	716							Q2TV78	MST1L_HUMAN	macrophage stimulating 1-like							extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)	p.P642L(1)									GCAGGCAAGTGGGCCCCCGTA	0.562																																					p.P642L		Atlas-SNP	.											Q13209_HUMAN,NS,carcinoma,0,1	.	.	1	1	Substitution - Missense(1)	endometrium(1)	c.C1925T						scavenged	.																																					11223	exon15			GCAAGTGGGCCCC	U28055, AF083416		1p36.33	2013-03-27	2012-11-09	2012-11-09	ENSG00000186715	ENSG00000186715			7390	other	unknown			"""macrophage stimulating, pseudogene 7"", ""macrophage stimulating, pseudogene 9"", ""macrophage stimulating 1 (hepatocyte growth factor-like) pseudogene 9"""	MSTP7, MSTP9, MST1P9		10728827	Standard	NM_001271733		Approved	D1F15S1A, MSPL7, MSPL-7	uc010ock.3	Q2TV78	OTTHUMG00000002578		1.37:g.17083872G>A		Somatic	719	3	0.00417246		WXS	Illumina HiSeq	Phase_I	698	15	0.02149	NM_001271733	B7WPB1|Q13209	Missense_Mutation	SNP	ENST00000455405.2	37		.	.	.	.	.	.	.	.	.	.	.	13.44	2.237181	0.39498	.	.	ENSG00000186715	ENST00000334998;ENST00000442552	.	.	.	.	.	.	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.000000	0.41823	D	0.000805	T	0.66197	0.2765	.	.	.	.	.	.	D;D	0.89917	0.999;1.0	D;D	0.97110	0.989;1.0	T	0.72117	-0.4387	6	0.87932	D	0	.	6.7402	0.23431	2.0E-4:0.0:0.9998:0.0	rs61635893	642;668	Q2TV78-2;Q2TV78	.;MSTP9_HUMAN	L	642;668	.	ENSP00000439273:P642L	P	-	2	0	MST1P9	16956459	1.000000	0.71417	0.997000	0.53966	0.000000	0.00434	5.900000	0.69853	0.502000	0.28037	0.000000	0.15137	CCA	.	.	weak		0.562	MST1L-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000400328.1	NM_001271733	
HYLS1	219844	hgsc.bcm.edu	37	11	125769354	125769354	+	Missense_Mutation	SNP	T	T	C	rs667782	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr11:125769354T>C	ENST00000425380.2	+	3	872	c.91T>C	c.(91-93)Tgt>Cgt	p.C31R	HYLS1_ENST00000356438.3_Missense_Mutation_p.C31R|PUS3_ENST00000227474.3_Intron|HYLS1_ENST00000526028.1_Missense_Mutation_p.C31R	NM_001134793.1	NP_001128265.1	Q96M11	HYLS1_HUMAN	hydrolethalus syndrome 1	31			C -> R (in dbSNP:rs667782). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.			centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|endometrium(1)|large_intestine(3)|skin(3)|upper_aerodigestive_tract(1)	9	all_hematologic(175;0.177)	Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.131)|all_lung(97;0.139)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.13e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0446)		TACCCACATCTGTGCAGGGCA	0.488													T|||	1499	0.299321	0.3177	0.2291	5008	,	,		19753	0.3542		0.2416	False		,,,				2504	0.3272				p.C31R	Esophageal Squamous(172;2590 2636 8884 10471)	Atlas-SNP	.											.	HYLS1	25	.	0			c.T91C						PASS	.	T	ARG/CYS,,ARG/CYS	1325,3077	444.1+/-347.2	212,901,1088	86.0	79.0	81.0		91,,91	6.2	1.0	11	dbSNP_83	81	2046,6552	356.6+/-330.4	255,1536,2508	yes	missense,intron,missense	PUS3,HYLS1	NM_001134793.1,NM_031307.3,NM_145014.2	180,,180	467,2437,3596	CC,CT,TT		23.7962,30.1,25.9308	possibly-damaging,,possibly-damaging	31/300,,31/300	125769354	3371,9629	2201	4299	6500	SO:0001583	missense	219844	exon3			CACATCTGTGCAG	AK057477	CCDS8467.1	11q24	2014-06-18				ENSG00000198331			26558	protein-coding gene	gene with protein product		610693				15843405	Standard	NM_145014		Approved	FLJ32915	uc009zbv.3	Q96M11		ENST00000425380.2:c.91T>C	11.37:g.125769354T>C	ENSP00000414884:p.Cys31Arg	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	116	5	0.0431034	NM_001134793	B3KXI8|Q96BX9	Missense_Mutation	SNP	ENST00000425380.2	37	CCDS8467.1	650	0.2976190476190476	171	0.3475609756097561	70	0.19337016574585636	211	0.3688811188811189	198	0.2612137203166227	T	18.54	3.646288	0.67358	0.301	0.237962	ENSG00000198331	ENST00000356438;ENST00000425380;ENST00000526028	T;T;T	0.74106	-0.81;-0.81;-0.81	6.17	6.17	0.99709	.	0.269718	0.30201	N	0.010162	T	0.00012	0.0000	L	0.51422	1.61	0.09310	P	1.0	P	0.45212	0.853	P	0.47528	0.549	T	0.04509	-1.0946	9	0.72032	D	0.01	.	15.0521	0.71881	0.0:0.0:0.0:1.0	rs667782;rs17845455;rs17858328;rs52828124;rs59008206;rs667782	31	Q96M11	HYLS1_HUMAN	R	31	ENSP00000348815:C31R;ENSP00000414884:C31R;ENSP00000436833:C31R	ENSP00000348815:C31R	C	+	1	0	HYLS1	125274564	1.000000	0.71417	0.999000	0.59377	0.906000	0.53458	4.052000	0.57420	2.371000	0.80710	0.533000	0.62120	TGT	T|0.719;C|0.281	0.281	strong		0.488	HYLS1-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386733.1	NM_145014	
CARF	79800	hgsc.bcm.edu	37	2	203846817	203846817	+	Missense_Mutation	SNP	A	A	T	rs72932557	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr2:203846817A>T	ENST00000402905.3	+	15	2033	c.1712A>T	c.(1711-1713)tAc>tTc	p.Y571F	CARF_ENST00000545253.1_Missense_Mutation_p.Y483F|WDR12_ENST00000477723.1_Intron|CARF_ENST00000428585.1_Missense_Mutation_p.Y495F|CARF_ENST00000545262.1_Missense_Mutation_p.Y495F|CARF_ENST00000438828.2_Missense_Mutation_p.Y571F|CARF_ENST00000414439.1_Missense_Mutation_p.Y469F|CARF_ENST00000320443.8_Missense_Mutation_p.Y571F	NM_001104586.1|NM_001282910.1|NM_001282911.1|NM_001282912.1	NP_001098056.1|NP_001269839.1|NP_001269840.1|NP_001269841.1	Q8N187	CARTF_HUMAN	calcium responsive transcription factor	571					cellular response to calcium ion (GO:0071277)|cellular response to potassium ion (GO:0035865)|positive regulation of transcription from RNA polymerase II promoter in response to calcium ion (GO:0061400)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)										CAACCAAGGTACACCTCTCCT	0.373													T|||	236	0.0471246	0.0174	0.0749	5008	,	,		18007	0.0159		0.1302	False		,,,				2504	0.0143				p.Y571F		Atlas-SNP	.											ALS2CR8,rectum,carcinoma,-1,1	ALS2CR8	56	1	0			c.A1712T						PASS	.	T	PHE/TYR,PHE/TYR	130,3558		2,126,1716	59.0	55.0	56.0		1712,1712	4.3	0.3	2	dbSNP_130	56	1055,7155		68,919,3118	yes	missense,missense	ALS2CR8	NM_001104586.1,NM_024744.14	22,22	70,1045,4834	TT,TA,AA		12.8502,3.5249,9.9597	benign,benign	571/726,571/726	203846817	1185,10713	1844	4105	5949	SO:0001583	missense	79800	exon16			CAAGGTACACCTC	AB053309	CCDS42801.1, CCDS63091.1	2q33.3	2013-06-12	2013-06-12	2013-06-12	ENSG00000138380	ENSG00000138380			14435	protein-coding gene	gene with protein product	"""calcium-response factor"""	607586	"""amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 8"""	ALS2CR8		11586298, 11832226	Standard	XM_005246858		Approved	FLJ21579, CaRF, NYD-SP24	uc002uzo.2	Q8N187	OTTHUMG00000154528	ENST00000402905.3:c.1712A>T	2.37:g.203846817A>T	ENSP00000384006:p.Tyr571Phe	Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	82	4	0.0487805	NM_024744	B4E1W7|G3V1K7|Q8ND29|Q8WXC0|Q96J78|Q96Q38|Q96Q39|Q9H712	Missense_Mutation	SNP	ENST00000402905.3	37	CCDS42801.1	160	0.07326007326007326	9	0.018292682926829267	34	0.09392265193370165	13	0.022727272727272728	104	0.13720316622691292	T	3.052	-0.195095	0.06259	0.035249	0.128502	ENSG00000138380	ENST00000402905;ENST00000414439;ENST00000428585;ENST00000545253;ENST00000545262;ENST00000320443;ENST00000438828	.	.	.	5.45	4.26	0.50523	.	0.229295	0.37715	N	0.001971	T	0.00073	0.0002	N	0.00237	-1.79	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.24012	-1.0172	8	0.02654	T	1	0.0747	8.9639	0.35865	0.297:0.0:0.0:0.703	.	483;495;571	B4DIA7;G3V1K7;Q8N187	.;.;AL2S8_HUMAN	F	571;469;495;483;495;571;571	.	ENSP00000316224:Y571F	Y	+	2	0	ALS2CR8	203555062	0.839000	0.29477	0.278000	0.24718	0.867000	0.49689	0.917000	0.28665	0.341000	0.23771	-0.257000	0.10917	TAC	A|0.910;T|0.090	0.090	strong		0.373	CARF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335768.5	NM_001104586	
TPPP	11076	hgsc.bcm.edu	37	5	678087	678087	+	Missense_Mutation	SNP	C	C	T	rs570878136	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr5:678087C>T	ENST00000360578.5	-	2	210	c.89G>A	c.(88-90)aGg>aAg	p.R30K	CTD-2589H19.6_ENST00000607068.1_RNA	NM_007030.2	NP_008961.1	O94811	TPPP_HUMAN	tubulin polymerization promoting protein	30	Mediates interaction with LIMK1.				microtubule bundle formation (GO:0001578)|microtubule polymerization (GO:0046785)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of protein polymerization (GO:0032273)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	microtubule binding (GO:0008017)|tubulin binding (GO:0015631)	p.R30K(1)		kidney(1)|large_intestine(1)|lung(2)|prostate(1)	5		Ovarian(839;0.0563)	Epithelial(17;0.000445)|all cancers(22;0.00176)|OV - Ovarian serous cystadenocarcinoma(19;0.00227)|Lung(60;0.0863)	GBM - Glioblastoma multiforme(108;0.0191)		CAGCGACAGCCTCTTGGCTGC	0.677													C|||	15	0.00299521	0.0061	0.0	5008	,	,		16462	0.0069		0.0	False		,,,				2504	0.0				p.R30K		Atlas-SNP	.											TPPP,NS,carcinoma,0,1	TPPP	24	1	1	Substitution - Missense(1)	prostate(1)	c.G89A						scavenged	.						14.0	17.0	16.0					5																	678087		2199	4295	6494	SO:0001583	missense	11076	exon2			GACAGCCTCTTGG	AB017016	CCDS3856.1	5p15.33	2008-02-05			ENSG00000171368	ENSG00000171368			24164	protein-coding gene	gene with protein product	"""brain specific protein p25 alpha"""	608773				10083737, 12093283, 15590652, 17105200	Standard	NM_007030		Approved	p25alpha, TPPP1, p25, TPPP/p25	uc003jbh.4	O94811	OTTHUMG00000131011	ENST00000360578.5:c.89G>A	5.37:g.678087C>T	ENSP00000353785:p.Arg30Lys	Somatic	225	4	0.0177778		WXS	Illumina HiSeq	Phase_I	248	11	0.0443548	NM_007030		Missense_Mutation	SNP	ENST00000360578.5	37	CCDS3856.1	.	.	.	.	.	.	.	.	.	.	c	14.67	2.605282	0.46423	.	.	ENSG00000171368	ENST00000360578	T	0.45276	0.9	5.23	5.23	0.72850	.	0.149935	0.44902	D	0.000407	T	0.29588	0.0738	L	0.29908	0.895	0.44635	D	0.997618	B	0.15141	0.012	B	0.13407	0.009	T	0.11867	-1.0570	10	0.05436	T	0.98	-54.1656	16.5545	0.84482	0.0:1.0:0.0:0.0	.	30	O94811	TPPP_HUMAN	K	30	ENSP00000353785:R30K	ENSP00000353785:R30K	R	-	2	0	TPPP	731087	1.000000	0.71417	0.998000	0.56505	0.405000	0.30901	4.081000	0.57627	2.437000	0.82529	0.491000	0.48974	AGG	.	.	none		0.677	TPPP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253645.3	NM_007030	
RSPH3	83861	hgsc.bcm.edu	37	6	159399348	159399348	+	Missense_Mutation	SNP	A	A	G	rs768994	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr6:159399348A>G	ENST00000252655.1	-	7	1505	c.1316T>C	c.(1315-1317)aTg>aCg	p.M439T	RSPH3_ENST00000449822.1_Missense_Mutation_p.M201T|RSPH3_ENST00000607398.1_5'Flank|RSPH3_ENST00000367069.2_Missense_Mutation_p.M297T|RSPH3_ENST00000297262.3_Missense_Mutation_p.M343T	NM_031924.4	NP_114130.3	Q86UC2	RSPH3_HUMAN	radial spoke 3 homolog (Chlamydomonas)	439			M -> T (in dbSNP:rs768994).					p.M439T(1)		endometrium(3)|kidney(2)|large_intestine(1)|lung(7)|ovary(2)|skin(1)|stomach(7)	23		Breast(66;0.00519)|Ovarian(120;0.123)		OV - Ovarian serous cystadenocarcinoma(65;2.36e-16)|BRCA - Breast invasive adenocarcinoma(81;5.92e-06)		AACTTCATTCATTAGCCATGG	0.299													A|||	981	0.195887	0.0492	0.3429	5008	,	,		14515	0.3919		0.0765	False		,,,				2504	0.2106				p.M439T		Atlas-SNP	.											RSPH3,NS,carcinoma,0,1	RSPH3	48	1	1	Substitution - Missense(1)	stomach(1)	c.T1316C						scavenged	.	A	THR/MET	307,4095	164.4+/-196.0	9,289,1903	58.0	56.0	57.0		1316	5.6	1.0	6	dbSNP_86	57	712,7862	171.7+/-222.6	37,638,3612	yes	missense	RSPH3	NM_031924.4	81	46,927,5515	GG,GA,AA		8.3042,6.9741,7.853	probably-damaging	439/561	159399348	1019,11957	2201	4287	6488	SO:0001583	missense	83861	exon7			TCATTCATTAGCC	AF353618	CCDS5260.1	6q25.3	2014-05-16	2008-07-04	2007-06-26	ENSG00000130363	ENSG00000130363			21054	protein-coding gene	gene with protein product		615876	"""radial spokehead-like 2"""	RSHL2		12477932	Standard	NM_031924		Approved	dJ111C20.1, RSP3	uc003qrx.3	Q86UC2	OTTHUMG00000015924	ENST00000252655.1:c.1316T>C	6.37:g.159399348A>G	ENSP00000252655:p.Met439Thr	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	89	3	0.0337079	NM_031924	Q96LQ5|Q96LX2|Q9BX75	Missense_Mutation	SNP	ENST00000252655.1	37	CCDS5260.1	422	0.19322344322344323	24	0.04878048780487805	94	0.2596685082872928	244	0.42657342657342656	60	0.079155672823219	A	19.24	3.789284	0.70337	0.069741	0.083042	ENSG00000130363	ENST00000367069;ENST00000449822;ENST00000252655;ENST00000297262	T;T;T;T	0.18174	2.23;2.23;2.23;2.23	5.57	5.57	0.84162	.	0.083199	0.85682	D	0.000000	T	0.20088	0.0483	M	0.73430	2.235	0.09310	P	0.99999176289	P;P	0.41232	0.724;0.743	B;P	0.47075	0.376;0.536	T	0.02333	-1.1175	9	0.41790	T	0.15	-24.6425	15.3989	0.74823	1.0:0.0:0.0:0.0	rs768994;rs52797265;rs60633343;rs768994	343;439	Q86UC2-2;Q86UC2	.;RSPH3_HUMAN	T	297;201;439;343	ENSP00000356036:M297T;ENSP00000393195:M201T;ENSP00000252655:M439T;ENSP00000297262:M343T	ENSP00000252655:M439T	M	-	2	0	RSPH3	159319336	1.000000	0.71417	0.998000	0.56505	0.998000	0.95712	8.445000	0.90326	2.124000	0.65301	0.477000	0.44152	ATG	A|0.862;G|0.138	0.138	strong		0.299	RSPH3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_031924	
DAAM1	23002	hgsc.bcm.edu	37	14	59797397	59797397	+	Silent	SNP	G	G	A			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr14:59797397G>A	ENST00000395125.1	+	12	1574	c.1551G>A	c.(1549-1551)gaG>gaA	p.E517E	DAAM1_ENST00000360909.3_Silent_p.E517E|DAAM1_ENST00000351081.1_Silent_p.E517E	NM_014992.2	NP_055807.1	Q9Y4D1	DAAM1_HUMAN	dishevelled associated activator of morphogenesis 1	517					actin cytoskeleton organization (GO:0030036)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)	identical protein binding (GO:0042802)			breast(3)|cervix(3)|endometrium(5)|kidney(5)|large_intestine(4)|lung(7)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(4)|urinary_tract(1)	37				OV - Ovarian serous cystadenocarcinoma(108;0.165)		AGCTCCATGAGCTCAGCAGGG	0.527																																					p.E517E		Atlas-SNP	.											.	DAAM1	95	.	0			c.G1551A						PASS	.						56.0	57.0	57.0					14																	59797397		2203	4300	6503	SO:0001819	synonymous_variant	23002	exon13			CCATGAGCTCAGC	AB014566	CCDS9737.1, CCDS58323.1	14q22.3	2008-08-11			ENSG00000100592	ENSG00000100592			18142	protein-coding gene	gene with protein product		606626				11779461, 18162551	Standard	NM_014992		Approved	KIAA0666	uc031qou.1	Q9Y4D1	OTTHUMG00000140326	ENST00000395125.1:c.1551G>A	14.37:g.59797397G>A		Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	166	53	0.319277	NM_001270520	Q86U34|Q8N1Z8|Q8TB39	Silent	SNP	ENST00000395125.1	37	CCDS9737.1																																																																																			.	.	none		0.527	DAAM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276942.2	NM_014992	
FAM135A	57579	hgsc.bcm.edu	37	6	71238105	71238105	+	Missense_Mutation	SNP	A	A	G	rs2747701	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr6:71238105A>G	ENST00000418814.2	+	16	4339	c.3725A>G	c.(3724-3726)gAt>gGt	p.D1242G	FAM135A_ENST00000457062.2_Missense_Mutation_p.D1029G|FAM135A_ENST00000361499.3_Missense_Mutation_p.D1046G|FAM135A_ENST00000505769.1_Missense_Mutation_p.D822G|FAM135A_ENST00000505868.1_Missense_Mutation_p.D1242G|FAM135A_ENST00000370479.3_Missense_Mutation_p.D1029G	NM_001105531.2|NM_001162529.1	NP_001099001.1|NP_001156001.1	Q9P2D6	F135A_HUMAN	family with sequence similarity 135, member A	1242			D -> G (in dbSNP:rs2747701). {ECO:0000269|PubMed:11230166, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:16192744}.							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						GAAGAAGAGGATGGTTCTGAA	0.403													A|||	1699	0.339257	0.0189	0.2507	5008	,	,		16392	0.5427		0.4761	False		,,,				2504	0.4847				p.D1242G		Atlas-SNP	.											.	FAM135A	181	.	0			c.A3725G						PASS	.	A	GLY/ASP,GLY/ASP,GLY/ASP	381,4025	192.3+/-217.7	13,355,1835	215.0	183.0	194.0		3137,3725,3086	3.8	0.7	6	dbSNP_100	194	4138,4462	564.9+/-388.4	1003,2132,1165	yes	missense,missense,missense	FAM135A	NM_001105531.2,NM_001162529.1,NM_020819.4	94,94,94	1016,2487,3000	GG,GA,AA		48.1163,8.6473,34.7455	benign,benign,benign	1046/1320,1242/1516,1029/1303	71238105	4519,8487	2203	4300	6503	SO:0001583	missense	57579	exon14			AAGAGGATGGTTC	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.3725A>G	6.37:g.71238105A>G	ENSP00000410768:p.Asp1242Gly	Somatic	179	0	0		WXS	Illumina HiSeq	Phase_I	198	9	0.0454545	NM_001162529	A2RRQ5|Q3C0H3|Q5JXK0|Q5JXK1|Q68DW0|Q6P081|Q9H0F2|Q9NU48|Q9NUQ5|Q9NXL5	Missense_Mutation	SNP	ENST00000418814.2	37	CCDS55028.1	779	0.3566849816849817	12	0.024390243902439025	98	0.27071823204419887	305	0.5332167832167832	364	0.48021108179419525	A	12.22	1.872457	0.33069	0.086473	0.481163	ENSG00000082269	ENST00000418814;ENST00000370479;ENST00000505769;ENST00000457062;ENST00000361499;ENST00000505868	T;T;T;T;T;T	0.24538	2.16;2.16;1.85;2.16;2.16;2.15	4.92	3.77	0.43336	.	0.230845	0.51477	N	0.000093	T	0.14874	0.0359	M	0.67953	2.075	0.09310	P	0.99999351703	B;B;B;B;B	0.31040	0.305;0.11;0.067;0.076;0.11	B;B;B;B;B	0.33042	0.109;0.157;0.075;0.047;0.157	T	0.04053	-1.0981	9	0.59425	D	0.04	.	10.304	0.43670	0.9221:0.0:0.0779:0.0	rs2747701;rs3736753;rs60825985;rs2747701	822;1242;1242;1046;1029	D6RCC7;Q9P2D6-4;Q9P2D6;Q9P2D6-2;Q9P2D6-3	.;.;F135A_HUMAN;.;.	G	1242;1029;822;1029;1046;1242	ENSP00000410768:D1242G;ENSP00000359510:D1029G;ENSP00000423785:D822G;ENSP00000409201:D1029G;ENSP00000354913:D1046G;ENSP00000423307:D1242G	ENSP00000354913:D1046G	D	+	2	0	FAM135A	71294826	1.000000	0.71417	0.723000	0.30687	0.305000	0.27757	6.153000	0.71819	0.843000	0.35070	0.482000	0.46254	GAT	A|0.647;G|0.353	0.353	strong		0.403	FAM135A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000041137.2	NM_020819	
PRAMEF4	400735	hgsc.bcm.edu	37	1	12939782	12939782	+	Silent	SNP	A	A	G	rs200129543		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr1:12939782A>G	ENST00000235349.5	-	4	1090	c.1020T>C	c.(1018-1020)ctT>ctC	p.L340L		NM_001009611.2	NP_001009611.1	O60810	PRAM4_HUMAN	PRAME family member 4	340					negative regulation of apoptotic process (GO:0043066)|negative regulation of cell differentiation (GO:0045596)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)					breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(10)|ovary(2)|prostate(3)|skin(1)	24	Ovarian(185;0.249)	Lung NSC(185;3.67e-05)|all_lung(284;4.03e-05)|Renal(390;0.000147)|Breast(348;0.000278)|Colorectal(325;0.00058)|Ovarian(437;0.00965)|Hepatocellular(190;0.0245)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;4.88e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|COAD - Colon adenocarcinoma(227;0.000241)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		GGAGAGGCACAAGACTGTAAT	0.473																																					p.L340L		Atlas-SNP	.											PRAMEF4,NS,carcinoma,0,1	PRAMEF4	62	1	0			c.T1020C						scavenged	.																																			SO:0001819	synonymous_variant	400735	exon4			AGGCACAAGACTG		CCDS30592.1	1p36.21	2013-01-17			ENSG00000243073	ENSG00000243073		"""-"""	31971	protein-coding gene	gene with protein product							Standard	NM_001009611		Approved	RP5-845O24.6	uc001aun.2	O60810	OTTHUMG00000001987	ENST00000235349.5:c.1020T>C	1.37:g.12939782A>G		Somatic	20	3	0.15		WXS	Illumina HiSeq	Phase_I	25	7	0.28	NM_001009611	Q5LJB5	Silent	SNP	ENST00000235349.5	37	CCDS30592.1																																																																																			.	.	weak		0.473	PRAMEF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005518.1	NM_001009611	
KCTD10	83892	hgsc.bcm.edu	37	12	109889615	109889615	+	Missense_Mutation	SNP	C	C	G			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr12:109889615C>G	ENST00000228495.6	-	7	1008	c.727G>C	c.(727-729)Gag>Cag	p.E243Q	KCTD10_ENST00000540089.1_Missense_Mutation_p.E62Q|KCTD10_ENST00000424763.2_Missense_Mutation_p.E62Q|KCTD10_ENST00000538161.1_5'UTR|KCTD10_ENST00000540411.1_Missense_Mutation_p.E217Q	NM_031954.3	NP_114160.1	Q9H3F6	BACD3_HUMAN	potassium channel tetramerization domain containing 10	243					proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein homooligomerization (GO:0051260)|protein ubiquitination (GO:0016567)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|TCTN-B9D complex (GO:0036038)				endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(1)	10						TCGGGAAACTCCACCTGTGTT	0.582																																					p.E243Q		Atlas-SNP	.											KCTD10,NS,carcinoma,0,1	KCTD10	24	1	0			c.G727C						PASS	.						25.0	28.0	27.0					12																	109889615		2203	4300	6503	SO:0001583	missense	83892	exon7			GAAACTCCACCTG	BC040062	CCDS9128.1	12q24.12	2013-06-20	2013-06-20		ENSG00000110906	ENSG00000110906		"""BTB/POZ domain containing"""	23236	protein-coding gene	gene with protein product		613421	"""potassium channel tetramerisation domain containing 10"""			12477932	Standard	XM_005253946		Approved	MSTP028, BTBD28	uc001toi.1	Q9H3F6	OTTHUMG00000169253	ENST00000228495.6:c.727G>C	12.37:g.109889615C>G	ENSP00000228495:p.Glu243Gln	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	71	24	0.338028	NM_031954	Q53HN2|Q59FV1|Q6PL47|Q96SU0	Missense_Mutation	SNP	ENST00000228495.6	37	CCDS9128.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	21.4|21.4	4.138586|4.138586	0.77775|0.77775	.|.	.|.	ENSG00000110906|ENSG00000110906	ENST00000228495;ENST00000540089;ENST00000545759;ENST00000424763;ENST00000540411;ENST00000542954;ENST00000535546;ENST00000540402;ENST00000540355|ENST00000538161	T;T|.	0.58060|.	0.51;0.36|.	4.97|4.97	4.97|4.97	0.65823|0.65823	.|.	0.051633|.	0.85682|.	D|.	0.000000|.	T|T	0.79275|0.79275	0.4418|0.4418	M|M	0.83953|0.83953	2.67|2.67	0.80722|0.80722	D|D	1|1	D;D;D|.	0.89917|.	0.999;1.0;0.998|.	D;D;D|.	0.83275|.	0.988;0.996;0.974|.	T|T	0.80683|0.80683	-0.1273|-0.1273	10|5	0.87932|.	D|.	0|.	-31.0378|-31.0378	17.765|17.765	0.88475|0.88475	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	217;220;243|.	F5GWA4;Q9H3F6-2;Q9H3F6|.	.;.;BACD3_HUMAN|.	Q|C	243;62;85;62;217;62;62;62;62|208	ENSP00000228495:E243Q;ENSP00000441672:E217Q|.	ENSP00000228495:E243Q|.	E|W	-|-	1|3	0|0	KCTD10|KCTD10	108373998|108373998	1.000000|1.000000	0.71417|0.71417	0.988000|0.988000	0.46212|0.46212	0.476000|0.476000	0.33039|0.33039	7.622000|7.622000	0.83099|0.83099	2.757000|2.757000	0.94681|0.94681	0.655000|0.655000	0.94253|0.94253	GAG|TGG	.	.	none		0.582	KCTD10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403099.1	NM_031954	
CMYA5	202333	hgsc.bcm.edu	37	5	79030212	79030212	+	Missense_Mutation	SNP	C	C	T	rs16877147	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr5:79030212C>T	ENST00000446378.2	+	2	5655	c.5624C>T	c.(5623-5625)gCg>gTg	p.A1875V		NM_153610.3	NP_705838.3	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	1875			A -> V (in dbSNP:rs16877147).		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)		p.A1875V(1)		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)		ACCAAGCCTGCGGATGTCAAA	0.368													c|||	635	0.126797	0.0749	0.036	5008	,	,		21651	0.3621		0.0606	False		,,,				2504	0.0869				p.A1875V		Atlas-SNP	.											CMYA5,NS,carcinoma,0,1	CMYA5	643	1	1	Substitution - Missense(1)	stomach(1)	c.C5624T						scavenged	.	T	VAL/ALA	220,3420		13,194,1613	70.0	68.0	68.0		5624	-1.7	0.0	5	dbSNP_123	68	538,7634		22,494,3570	yes	missense	CMYA5	NM_153610.3	64	35,688,5183	TT,TC,CC		6.5835,6.044,6.4172	benign	1875/4070	79030212	758,11054	1820	4086	5906	SO:0001583	missense	202333	exon2			AGCCTGCGGATGT	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.5624C>T	5.37:g.79030212C>T	ENSP00000394770:p.Ala1875Val	Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	190	4	0.0210526	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	338	0.15476190476190477	49	0.09959349593495935	12	0.03314917127071823	232	0.40559440559440557	45	0.059366754617414245	c	10.65	1.411075	0.25465	0.06044	0.065835	ENSG00000164309	ENST00000446378	T	0.08008	3.14	6.06	-1.69	0.08186	.	1.442290	0.04201	N	0.330014	T	0.00012	0.0000	N	0.17082	0.46	0.80722	P	0.0	B	0.14438	0.01	B	0.10450	0.005	T	0.43065	-0.9414	9	0.02654	T	1	.	3.5465	0.07831	0.1033:0.5421:0.1109:0.2437	rs16877147;rs16877147	1875	Q8N3K9	CMYA5_HUMAN	V	1875	ENSP00000394770:A1875V	ENSP00000394770:A1875V	A	+	2	0	CMYA5	79065968	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.127000	0.15790	-0.228000	0.09869	-2.083000	0.00378	GCG	C|0.851;T|0.149	0.149	strong		0.368	CMYA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369497.1	NM_153610	
WWP2	11060	hgsc.bcm.edu	37	16	69967897	69967897	+	Silent	SNP	T	T	C	rs2270841	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr16:69967897T>C	ENST00000359154.2	+	17	1808	c.1707T>C	c.(1705-1707)caT>caC	p.H569H	WWP2_ENST00000542271.1_Silent_p.H453H|WWP2_ENST00000568684.1_Silent_p.H130H|WWP2_ENST00000448661.1_Silent_p.H569H|WWP2_ENST00000544162.1_3'UTR|MIR140_ENST00000385282.1_RNA|WWP2_ENST00000356003.2_Silent_p.H569H	NM_001270454.1|NM_007014.4	NP_001257383.1|NP_008945.2	O00308	WWP2_HUMAN	WW domain containing E3 ubiquitin protein ligase 2	569	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				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						TCCTGTCTCATGAGGTGCTCA	0.483													C|||	4280	0.854633	0.947	0.7507	5008	,	,		23109	0.9683		0.7525	False		,,,				2504	0.7914				p.H569H		Atlas-SNP	.											WWP2,NS,carcinoma,0,1	WWP2	88	1	0			c.T1707C						PASS	.	C	,	3941,455	218.1+/-236.3	1767,407,24	186.0	170.0	175.0		1707,390	-3.6	0.8	16	dbSNP_100	175	6380,2220	378.8+/-339.0	2378,1624,298	no	coding-synonymous,coding-synonymous	WWP2	NM_007014.3,NM_199424.1	,	4145,2031,322	CC,CT,TT		25.814,10.3503,20.5833	,	569/871,130/432	69967897	10321,2675	2198	4300	6498	SO:0001819	synonymous_variant	11060	exon17			GTCTCATGAGGTG	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.1707T>C	16.37:g.69967897T>C		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	85	6	0.0705882	NM_001270454	A6NEP1|B2R706|B4DTL5|F5H213|H3BRF3|I3RSG8|Q6ZTQ5|Q96CZ2|Q9BWN6	Silent	SNP	ENST00000359154.2	37	CCDS10885.1																																																																																			T|0.194;C|0.806	0.806	strong		0.483	WWP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268954.1	NM_007014	
RSPH3	83861	hgsc.bcm.edu	37	6	159398633	159398633	+	Silent	SNP	T	T	C	rs3756988	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr6:159398633T>C	ENST00000252655.1	-	8	1809	c.1620A>G	c.(1618-1620)gaA>gaG	p.E540E	RSPH3_ENST00000449822.1_Silent_p.E302E|RSPH3_ENST00000607398.1_5'Flank|RSPH3_ENST00000367069.2_Silent_p.E398E|RSPH3_ENST00000297262.3_Silent_p.E444E	NM_031924.4	NP_114130.3	Q86UC2	RSPH3_HUMAN	radial spoke 3 homolog (Chlamydomonas)	540								p.E540E(1)		endometrium(3)|kidney(2)|large_intestine(1)|lung(7)|ovary(2)|skin(1)|stomach(7)	23		Breast(66;0.00519)|Ovarian(120;0.123)		OV - Ovarian serous cystadenocarcinoma(65;2.36e-16)|BRCA - Breast invasive adenocarcinoma(81;5.92e-06)		GCCCTAAGAGTTCTCTCTCTT	0.448													C|||	1064	0.21246	0.0651	0.3746	5008	,	,		18032	0.3919		0.1034	False		,,,				2504	0.2239				p.E540E		Atlas-SNP	.											RSPH3,NS,carcinoma,0,1	RSPH3	48	1	1	Substitution - coding silent(1)	stomach(1)	c.A1620G						PASS	.	C		404,4002	788.9+/-415.0	12,380,1811	261.0	246.0	251.0		1620	-5.7	0.0	6	dbSNP_107	251	926,7674	777.0+/-407.7	61,804,3435	no	coding-synonymous	RSPH3	NM_031924.4		73,1184,5246	CC,CT,TT		10.7674,9.1693,10.226		540/561	159398633	1330,11676	2203	4300	6503	SO:0001819	synonymous_variant	83861	exon8			TAAGAGTTCTCTC	AF353618	CCDS5260.1	6q25.3	2014-05-16	2008-07-04	2007-06-26	ENSG00000130363	ENSG00000130363			21054	protein-coding gene	gene with protein product		615876	"""radial spokehead-like 2"""	RSHL2		12477932	Standard	NM_031924		Approved	dJ111C20.1, RSP3	uc003qrx.3	Q86UC2	OTTHUMG00000015924	ENST00000252655.1:c.1620A>G	6.37:g.159398633T>C		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	73	6	0.0821918	NM_031924	Q96LQ5|Q96LX2|Q9BX75	Silent	SNP	ENST00000252655.1	37	CCDS5260.1																																																																																			T|0.844;C|0.156	0.156	strong		0.448	RSPH3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_031924	
MYOM1	8736	hgsc.bcm.edu	37	18	3168816	3168816	+	Splice_Site	SNP	G	G	A	rs2230167	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr18:3168816G>A	ENST00000356443.4	-	9	1671	c.1338C>T	c.(1336-1338)aaC>aaT	p.N446N	MYOM1_ENST00000400569.3_Splice_Site_p.N446N|MYOM1_ENST00000261606.7_Splice_Site_p.N446N	NM_003803.3|NM_019856.1	NP_003794.3|NP_062830.1	P52179	MYOM1_HUMAN	myomesin 1	446	Ig-like C2-type 2.				muscle contraction (GO:0006936)	M band (GO:0031430)|striated muscle myosin thick filament (GO:0005863)	identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|structural constituent of muscle (GO:0008307)			NS(2)|autonomic_ganglia(1)|central_nervous_system(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(20)|ovary(4)|pancreas(1)|prostate(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	77						AAGACTCACCGTTTCTGTACC	0.438													A|||	1413	0.282149	0.3313	0.2061	5008	,	,		18941	0.2798		0.2356	False		,,,				2504	0.32				p.N446N		Atlas-SNP	.											.	MYOM1	192	.	0			c.C1338T						PASS	.	A	,	1167,2591		170,827,882	106.0	99.0	101.0		1338,1338	4.4	1.0	18	dbSNP_98	101	2179,6049		287,1605,2222	yes	coding-synonymous-near-splice,coding-synonymous-near-splice	MYOM1	NM_003803.3,NM_019856.1	,	457,2432,3104	AA,AG,GG		26.4827,31.0538,27.9159	,	446/1686,446/1590	3168816	3346,8640	1879	4114	5993	SO:0001630	splice_region_variant	8736	exon9			CTCACCGTTTCTG	AF185573	CCDS45823.1, CCDS45824.1	18p11.31	2014-09-17	2012-10-17		ENSG00000101605	ENSG00000101605		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	7613	protein-coding gene	gene with protein product	"""skelemin"""	603508	"""myomesin 1 (skelemin) (185kD)"", ""myomesin 1 (skelemin) 185kDa"", ""myomesin 1, 185kDa"""			9806852	Standard	NM_019856		Approved		uc002klp.3	P52179	OTTHUMG00000178209	ENST00000356443.4:c.1339+1C>T	18.37:g.3168816G>A		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	122	5	0.0409836	NM_003803	Q14BD6|Q6H969|Q6ZUU0	Silent	SNP	ENST00000356443.4	37	CCDS45824.1																																																																																			T|0.125;G|0.436;C|0.285;A|0.154	0.154	strong		0.438	MYOM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441037.2	NM_003803	Silent
NBN	4683	hgsc.bcm.edu	37	8	90990479	90990479	+	Missense_Mutation	SNP	C	C	G	rs1805794	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr8:90990479C>G	ENST00000265433.3	-	5	707	c.553G>C	c.(553-555)Gag>Cag	p.E185Q	NBN_ENST00000409330.1_Missense_Mutation_p.E103Q	NM_002485.4	NP_002476.2	O60934	NBN_HUMAN	nibrin	185	Mediates interaction with SP100. {ECO:0000250}.		E -> Q (in dbSNP:rs1805794). {ECO:0000269|PubMed:14684699, ECO:0000269|PubMed:14688016, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:9590180, ECO:0000269|PubMed:9590181, ECO:0000269|Ref.7}.		blastocyst growth (GO:0001832)|cell cycle arrest (GO:0007050)|cell proliferation (GO:0008283)|DNA damage checkpoint (GO:0000077)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA duplex unwinding (GO:0032508)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|intrinsic apoptotic signaling pathway (GO:0097193)|isotype switching (GO:0045190)|meiotic nuclear division (GO:0007126)|mitotic cell cycle checkpoint (GO:0007093)|mitotic G2 DNA damage checkpoint (GO:0007095)|neuromuscular process controlling balance (GO:0050885)|positive regulation of kinase activity (GO:0033674)|positive regulation of protein autophosphorylation (GO:0031954)|regulation of DNA-dependent DNA replication initiation (GO:0030174)|telomere maintenance (GO:0000723)	Mre11 complex (GO:0030870)|nuclear chromosome, telomeric region (GO:0000784)|nuclear inclusion body (GO:0042405)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|replication fork (GO:0005657)|site of double-strand break (GO:0035861)	damaged DNA binding (GO:0003684)|protein N-terminus binding (GO:0047485)|transcription factor binding (GO:0008134)			autonomic_ganglia(1)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(2)|lung(7)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	27			BRCA - Breast invasive adenocarcinoma(11;0.0344)			TTCTTGGACTCAACTGCTTTC	0.299								Homologous recombination					G|||	1788	0.357029	0.2307	0.3761	5008	,	,		16191	0.4673		0.3062	False		,,,				2504	0.453				p.E185Q		Atlas-SNP	.											.	NBN	86	.	0			c.G553C	GRCh37	CM034886	NBN	M	rs1805794	PASS	.	G	GLN/GLU	1030,3376	725.4+/-409.6	125,780,1298	87.0	86.0	87.0		553	3.1	1.0	8	dbSNP_92	87	2697,5903	682.4+/-403.8	413,1871,2016	yes	missense	NBN	NM_002485.4	29	538,2651,3314	GG,GC,CC		31.3605,23.3772,28.656	benign	185/755	90990479	3727,9279	2203	4300	6503	SO:0001583	missense	4683	exon5			TGGACTCAACTGC	AF058696	CCDS6249.1	8q21-q24	2014-09-17	2005-06-02	2005-06-02	ENSG00000104320	ENSG00000104320			7652	protein-coding gene	gene with protein product		602667	"""Nijmegen breakage syndrome 1 (nibrin)"""	NBS, NBS1		9590181, 9590180	Standard	XM_005250923		Approved	ATV, AT-V2, AT-V1	uc003yej.1	O60934	OTTHUMG00000153546	ENST00000265433.3:c.553G>C	8.37:g.90990479C>G	ENSP00000265433:p.Glu185Gln	Somatic	231	0	0		WXS	Illumina HiSeq	Phase_I	219	9	0.0410959	NM_002485	B2R626|B2RNC5|O60672|Q32NF7|Q53FM6|Q63HR6|Q7LDM2	Missense_Mutation	SNP	ENST00000265433.3	37	CCDS6249.1	726	0.3324175824175824	110	0.22357723577235772	122	0.3370165745856354	261	0.4562937062937063	233	0.3073878627968338	G	3.805	-0.040880	0.07452	0.233772	0.313605	ENSG00000104320	ENST00000265433;ENST00000409330;ENST00000452387;ENST00000517772	T;T;T	0.71222	0.43;0.51;-0.55	5.96	3.08	0.35506	.	0.222293	0.47093	N	0.000243	T	0.00012	0.0000	N	0.01454	-0.855	0.53688	P	2.8000000000028002E-5	B	0.02656	0.0	B	0.04013	0.001	T	0.39623	-0.9605	9	0.02654	T	1	-2.2013	13.9393	0.64046	0.0:0.4497:0.4384:0.1119	rs1805794;rs3174084;rs1805794	185	O60934	NBN_HUMAN	Q	185;103;185;103	ENSP00000265433:E185Q;ENSP00000386924:E103Q;ENSP00000428717:E103Q	ENSP00000265433:E185Q	E	-	1	0	NBN	91059655	1.000000	0.71417	0.999000	0.59377	0.986000	0.74619	2.133000	0.42093	0.091000	0.17302	-0.120000	0.15030	GAG	C|0.681;G|0.319	0.319	strong		0.299	NBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331583.3	NM_001024688	
TRPC1	7220	hgsc.bcm.edu	37	3	142523349	142523349	+	Silent	SNP	G	G	A	rs3821647	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr3:142523349G>A	ENST00000476941.1	+	12	2517	c.2031G>A	c.(2029-2031)acG>acA	p.T677T	TRPC1_ENST00000273482.6_Silent_p.T643T	NM_001251845.1	NP_001238774.1	P48995	TRPC1_HUMAN	transient receptor potential cation channel, subfamily C, member 1	677					axon guidance (GO:0007411)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|response to calcium ion (GO:0051592)|saliva secretion (GO:0046541)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|costamere (GO:0043034)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|sarcomere (GO:0030017)	calcium channel activity (GO:0005262)|cation channel activity (GO:0005261)|inositol 1,4,5 trisphosphate binding (GO:0070679)|ion channel binding (GO:0044325)|store-operated calcium channel activity (GO:0015279)	p.T643T(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(18)|ovary(2)|skin(2)|stomach(3)|urinary_tract(1)	37						ACAAATGTACGTTACCTCCAC	0.368													G|||	972	0.194089	0.2186	0.1354	5008	,	,		16060	0.2391		0.2038	False		,,,				2504	0.1462				p.T677T		Atlas-SNP	.											TRPC1,NS,carcinoma,0,1	TRPC1	82	1	1	Substitution - coding silent(1)	stomach(1)	c.G2031A						scavenged	.	G		928,3478	352.6+/-311.8	97,734,1372	100.0	95.0	97.0		1929	-3.1	1.0	3	dbSNP_107	97	1578,7022	294.8+/-302.1	163,1252,2885	no	coding-synonymous	TRPC1	NM_003304.4		260,1986,4257	AA,AG,GG		18.3488,21.0622,19.268		643/760	142523349	2506,10500	2203	4300	6503	SO:0001819	synonymous_variant	7220	exon12			ATGTACGTTACCT	X89066	CCDS3126.1, CCDS58856.1	3q23	2011-12-14			ENSG00000144935	ENSG00000144935		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	12333	protein-coding gene	gene with protein product		602343				7568191, 16382100	Standard	NM_001251845		Approved	HTRP-1	uc003evc.3	P48995	OTTHUMG00000159301	ENST00000476941.1:c.2031G>A	3.37:g.142523349G>A		Somatic	207	0	0		WXS	Illumina HiSeq	Phase_I	229	6	0.0262009	NM_001251845	Q14CE4	Silent	SNP	ENST00000476941.1	37	CCDS58856.1																																																																																			G|0.806;A|0.194	0.194	strong		0.368	TRPC1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354520.1	NM_003304	
PLK4	10733	hgsc.bcm.edu	37	4	128814492	128814492	+	Silent	SNP	G	G	A	rs56250604	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr4:128814492G>A	ENST00000270861.5	+	11	2515	c.2241G>A	c.(2239-2241)ggG>ggA	p.G747G	PLK4_ENST00000515069.1_Silent_p.G669G|PLK4_ENST00000507249.1_Silent_p.G686G|PLK4_ENST00000514379.1_Silent_p.G706G|RNU6-583P_ENST00000516012.1_RNA|PLK4_ENST00000513090.1_Silent_p.G715G	NM_014264.4	NP_055079.3	O00444	PLK4_HUMAN	polo-like kinase 4	747					centriole replication (GO:0007099)|de novo centriole assembly (GO:0098535)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|positive regulation of centriole replication (GO:0046601)|protein phosphorylation (GO:0006468)|trophoblast giant cell differentiation (GO:0060707)	centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)|deuterosome (GO:0098536)|nucleolus (GO:0005730)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(10)|lung(12)|prostate(1)|upper_aerodigestive_tract(1)	31						AAAAGACAGGGAAGTCTTACA	0.299													G|||	363	0.072484	0.0	0.0836	5008	,	,		15010	0.2669		0.0199	False		,,,				2504	0.0164				p.G747G	Colon(135;508 1718 19061 31832 42879)	Atlas-SNP	.											.	PLK4	65	.	0			c.G2241A						PASS	.	G	,,	24,4382	25.3+/-52.1	0,24,2179	73.0	76.0	75.0		2145,2118,2241	0.6	0.7	4	dbSNP_129	75	105,8489	48.9+/-108.6	0,105,4192	no	coding-synonymous,coding-synonymous,coding-synonymous	PLK4	NM_001190799.1,NM_001190801.1,NM_014264.4	,,	0,129,6371	AA,AG,GG		1.2218,0.5447,0.9923	,,	715/939,706/930,747/971	128814492	129,12871	2203	4297	6500	SO:0001819	synonymous_variant	10733	exon11			GACAGGGAAGTCT	Y13115	CCDS3735.1, CCDS54803.1, CCDS54804.1	4q27-q28	2013-01-18	2010-06-24	2004-01-28	ENSG00000142731	ENSG00000142731			11397	protein-coding gene	gene with protein product		605031	"""serine/threonine kinase 18"", ""polo-like kinase 4 (Drosophila)"""	STK18			Standard	NM_014264		Approved	Sak	uc003ifo.3	O00444	OTTHUMG00000133301	ENST00000270861.5:c.2241G>A	4.37:g.128814492G>A		Somatic	463	0	0		WXS	Illumina HiSeq	Phase_I	480	22	0.0458333	NM_014264	B2RAL0|B7Z837|B7Z8G7|Q8IYF0|Q96Q95|Q9UD84|Q9UDE2	Silent	SNP	ENST00000270861.5	37	CCDS3735.1																																																																																			G|0.962;A|0.038	0.038	strong		0.299	PLK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257095.3		
ZNF35	7584	hgsc.bcm.edu	37	3	44692564	44692564	+	Missense_Mutation	SNP	C	C	G	rs2272044	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr3:44692564C>G	ENST00000396056.2	+	2	240	c.5C>G	c.(4-6)aCt>aGt	p.T2S	ZNF35_ENST00000399560.2_Missense_Mutation_p.T2S|ZNF35_ENST00000296092.3_Missense_Mutation_p.T2S|ZNF35_ENST00000542250.1_5'UTR|ZNF35_ENST00000453164.1_Missense_Mutation_p.T2S|RP11-944L7.4_ENST00000457331.1_RNA	NM_003420.3	NP_003411.3	P13682	ZNF35_HUMAN	zinc finger protein 35	2					cellular response to retinoic acid (GO:0071300)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cell (GO:0005623)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			large_intestine(3)|liver(2)|lung(4)|ovary(1)|prostate(1)|skin(1)	12		Ovarian(412;0.0228)		OV - Ovarian serous cystadenocarcinoma(275;2.49e-27)|KIRC - Kidney renal clear cell carcinoma(197;0.0475)|Kidney(197;0.0595)		GAGAAGATGACTGCAGAATTG	0.522													.|||	1579	0.315296	0.0076	0.2983	5008	,	,		19180	0.7907		0.1402	False		,,,				2504	0.4335				p.T2S		Atlas-SNP	.											.	ZNF35	34	.	0			c.C5G						PASS	.	C	SER/THR	170,4236	111.6+/-149.8	4,162,2037	37.0	39.0	39.0		5	4.1	1.0	3	dbSNP_100	39	1221,7379	245.0+/-274.0	94,1033,3173	no	missense	ZNF35	NM_003420.3	58	98,1195,5210	GG,GC,CC		14.1977,3.8584,10.6951	benign	2/528	44692564	1391,11615	2203	4300	6503	SO:0001583	missense	7584	exon2			AGATGACTGCAGA	X07289	CCDS2718.2	3p21.32	2013-01-08	2006-05-11		ENSG00000169981	ENSG00000169981		"""Zinc fingers, C2H2-type"""	13099	protein-coding gene	gene with protein product		194533	"""zinc finger protein 35 (clone HF.10)"""			2108922, 1572646	Standard	NM_003420		Approved	HF.10, HF10, Zfp105	uc003cnq.3	P13682	OTTHUMG00000133091	ENST00000396056.2:c.5C>G	3.37:g.44692564C>G	ENSP00000379368:p.Thr2Ser	Somatic	211	0	0		WXS	Illumina HiSeq	Phase_I	197	10	0.0507614	NM_003420	B2RBU6|Q53Y54|Q96D01	Missense_Mutation	SNP	ENST00000396056.2	37	CCDS2718.2	674	0.3086080586080586	4	0.008130081300813009	97	0.26795580110497236	462	0.8076923076923077	111	0.14643799472295516	C	18.92	3.725294	0.68959	0.038584	0.141977	ENSG00000169981	ENST00000396056;ENST00000415571;ENST00000432115;ENST00000296092;ENST00000399560;ENST00000453164	T	0.11385	2.78	4.08	4.08	0.47627	.	.	.	.	.	T	0.00012	0.0000	L	0.27053	0.805	0.09310	P	1.0	P	0.42409	0.779	B	0.34873	0.191	T	0.00557	-1.1672	8	0.87932	D	0	-11.5335	12.0697	0.53609	0.0:1.0:0.0:0.0	rs2272044;rs57973918	2	P13682	ZNF35_HUMAN	S	2	ENSP00000379368:T2S	ENSP00000296092:T2S	T	+	2	0	ZNF35	44667568	0.992000	0.36948	0.990000	0.47175	0.973000	0.67179	0.427000	0.21379	2.298000	0.77334	0.558000	0.71614	ACT	C|0.756;G|0.244	0.244	strong		0.522	ZNF35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256749.4	NM_003420	
AQP12B	653437	hgsc.bcm.edu	37	2	241622187	241622187	+	Missense_Mutation	SNP	C	C	T	rs4081909	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr2:241622187C>T	ENST00000407834.3	-	1	130	c.68G>A	c.(67-69)cGg>cAg	p.R23Q		NM_001102467.1	NP_001095937.1	A6NM10	AQ12B_HUMAN	aquaporin 12B	23						integral component of membrane (GO:0016021)	transporter activity (GO:0005215)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|lung(8)|ovary(1)	13		all_epithelial(40;1.71e-15)|Breast(86;2.14e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0294)|all_neural(83;0.0459)|Lung NSC(271;0.094)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;2.2e-31)|all cancers(36;1.08e-28)|OV - Ovarian serous cystadenocarcinoma(60;2.13e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;7.52e-06)|Lung(119;0.00163)|LUSC - Lung squamous cell carcinoma(224;0.008)|Colorectal(34;0.0124)|COAD - Colon adenocarcinoma(134;0.0757)		CTTGGAGGCCCGCCTGGCTGC	0.672													N|||	1096	0.21885	0.2436	0.3501	5008	,	,		16445	0.2649		0.1064	False		,,,				2504	0.1605				p.R23Q		Atlas-SNP	.											.	AQP12B	33	.	0			c.G68A						PASS	.		GLN/ARG	902,3468		188,526,1471	38.0	45.0	43.0		68	1.3	0.2	2	dbSNP_108	43	904,7658		152,600,3529	no	missense	AQP12B	NM_001102467.1	43	340,1126,5000	TT,TC,CC		10.5583,20.6407,13.9654	probably-damaging	23/308	241622187	1806,11126	2185	4281	6466	SO:0001583	missense	653437	exon1			GAGGCCCGCCTGG	BC041460	CCDS46560.1	2q37.3	2007-12-14	2005-05-26	2005-05-26	ENSG00000185176	ENSG00000185176		"""Ion channels / Aquaporins"""	6096	protein-coding gene	gene with protein product			"""insulin synthesis associated 3"""	INSSA3			Standard	NM_001102467		Approved		uc010fzj.3	A6NM10	OTTHUMG00000152263	ENST00000407834.3:c.68G>A	2.37:g.241622187C>T	ENSP00000384894:p.Arg23Gln	Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	151	14	0.0927152	NM_001102467	A4QPB9	Missense_Mutation	SNP	ENST00000407834.3	37	CCDS46560.1	405	0.18543956043956045	99	0.20121951219512196	93	0.2569060773480663	135	0.23601398601398602	78	0.10290237467018469	.	13.64	2.296236	0.40594	0.206407	0.105583	ENSG00000185176	ENST00000407834	T	0.11169	2.8	3.19	1.29	0.21616	.	0.556195	0.18450	N	0.140848	T	0.00012	0.0000	M	0.65498	2.005	0.50632	P	1.1899999999998023E-4	D	0.69078	0.997	P	0.54924	0.764	T	0.31558	-0.9939	8	.	.	.	0.0022	6.4343	0.21815	0.0:0.7311:0.0:0.2689	rs4081909	23	A6NM10-2	.	Q	23	ENSP00000384894:R23Q	.	R	-	2	0	AQP12B	241270860	0.000000	0.05858	0.173000	0.22940	0.190000	0.23558	-0.169000	0.09911	0.611000	0.30052	0.479000	0.44913	CGG	C|0.829;T|0.171	0.171	strong		0.672	AQP12B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325625.1		
MARCH10	162333	hgsc.bcm.edu	37	17	60821880	60821880	+	Missense_Mutation	SNP	G	G	T			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr17:60821880G>T	ENST00000311269.5	-	5	666	c.392C>A	c.(391-393)gCa>gAa	p.A131E	MARCH10_ENST00000544856.2_Missense_Mutation_p.A130E|MARCH10_ENST00000456609.2_Missense_Mutation_p.A131E|MARCH10_ENST00000583600.1_Missense_Mutation_p.A169E	NM_152598.2	NP_689811.2	Q8NA82	MARHA_HUMAN	membrane-associated ring finger (C3HC4) 10, E3 ubiquitin protein ligase	131					protein ubiquitination (GO:0016567)		ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(11)|liver(1)|lung(15)	38						AACCATTGGTGCTTGGTCTGC	0.428																																					p.A131E		Atlas-SNP	.											.	MARCH10	102	.	0			c.C392A						PASS	.						93.0	86.0	89.0					17																	60821880		2203	4300	6503	SO:0001583	missense	162333	exon5			ATTGGTGCTTGGT	AK093076	CCDS11635.1, CCDS74122.1, CCDS74123.1	17q23.3	2013-01-09	2012-02-23	2007-08-20		ENSG00000173838		"""RING-type (C3HC4) zinc fingers"", ""MARCH membrane-associated ring fingers"""	26655	protein-coding gene	gene with protein product		613337	"""ring finger protein 190"", ""membrane-associated ring finger (C3HC4) 10"""	RNF190		17604280	Standard	XM_005257103		Approved	FLJ35757, MARCH-X	uc002jag.4	Q8NA82		ENST00000311269.5:c.392C>A	17.37:g.60821880G>T	ENSP00000311496:p.Ala131Glu	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	52	14	0.269231	NM_001100875	D3DU09|Q8IYS7|Q8N7Z7	Missense_Mutation	SNP	ENST00000311269.5	37	CCDS11635.1	.	.	.	.	.	.	.	.	.	.	G	1.039	-0.679492	0.03353	.	.	ENSG00000173838	ENST00000456609;ENST00000311269;ENST00000544856	T;T;T	0.13089	2.66;2.66;2.62	4.02	-0.384	0.12474	.	1.015540	0.07895	N	0.971731	T	0.08980	0.0222	L	0.35723	1.085	0.09310	N	0.999999	B;B;B	0.18461	0.006;0.01;0.028	B;B;B	0.13407	0.004;0.009;0.009	T	0.42832	-0.9428	10	0.18710	T	0.47	-0.0502	3.2196	0.06711	0.205:0.0:0.4324:0.3626	.	130;130;131	B3KVK0;G3V1Q5;Q8NA82	.;.;MARHA_HUMAN	E	131;131;130	ENSP00000416177:A131E;ENSP00000311496:A131E;ENSP00000443746:A130E	ENSP00000311496:A131E	A	-	2	0	MARCH10	58175612	0.082000	0.21442	0.050000	0.19076	0.111000	0.19643	0.226000	0.17776	-0.006000	0.14370	0.561000	0.74099	GCA	.	.	none		0.428	MARCH10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000445252.1	NM_152598	
RNF145	153830	hgsc.bcm.edu	37	5	158630643	158630643	+	5'UTR	SNP	T	T	C			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr5:158630643T>C	ENST00000424310.2	-	0	342				RNF145_ENST00000519865.1_5'UTR|RNF145_ENST00000518802.1_Missense_Mutation_p.K25E|RNF145_ENST00000520638.1_Missense_Mutation_p.K9E|RNF145_ENST00000274542.2_Missense_Mutation_p.K23E|RNF145_ENST00000521606.2_Missense_Mutation_p.K12E	NM_001199383.1	NP_001186312.1	Q96MT1	RN145_HUMAN	ring finger protein 145							integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)			endometrium(7)|kidney(2)|large_intestine(5)|lung(9)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	30	Renal(175;0.00196)	Medulloblastoma(196;0.0523)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			ttttttttctttttttttttc	0.363																																					p.K25E		Atlas-SNP	.											RNF145,NS,carcinoma,+1,2	RNF145	110	2	0			c.A73G						scavenged	.						31.0	34.0	33.0					5																	158630643		2203	4300	6503	SO:0001623	5_prime_UTR_variant	153830	exon2			TTTTCTTTTTTTT	BC042684	CCDS4344.1, CCDS56390.1, CCDS56391.1, CCDS56392.1, CCDS56393.1	5q33.3	2013-01-09			ENSG00000145860	ENSG00000145860		"""RING-type (C3HC4) zinc fingers"""	20853	protein-coding gene	gene with protein product							Standard	NM_001199380		Approved	FLJ31951	uc003lxo.2	Q96MT1	OTTHUMG00000130306	ENST00000424310.2:c.-18A>G	5.37:g.158630643T>C		Somatic	71	1	0.0140845		WXS	Illumina HiSeq	Phase_I	67	2	0.0298507	NM_001199380	B7Z903|B7Z949|E7EVI7|Q8IVP7	Missense_Mutation	SNP	ENST00000424310.2	37	CCDS56390.1	.	.	.	.	.	.	.	.	.	.	T	5.631	0.301084	0.10678	.	.	ENSG00000145860	ENST00000274542;ENST00000521606;ENST00000413445;ENST00000518802;ENST00000520638	T;T;T;T;T	0.77098	-1.06;-1.04;-1.04;-1.07;-1.03	2.6	1.39	0.22231	.	6.604780	0.00166	N	0.000010	T	0.60663	0.2286	N	0.08118	0	0.09310	N	0.999998	B;B;B;B;B	0.10296	0.003;0.001;0.001;0.001;0.001	B;B;B;B;B	0.04013	0.001;0.0;0.001;0.001;0.001	T	0.51553	-0.8691	10	0.54805	T	0.06	.	4.5107	0.11910	0.0:0.1769:0.0:0.8231	.	11;12;9;25;23	E7EW26;B7Z949;B7Z903;E7EVI7;Q96MT1-2	.;.;.;.;.	E	23;11;12;25;9	ENSP00000274542:K23E;ENSP00000430753:K11E;ENSP00000445115:K12E;ENSP00000430955:K25E;ENSP00000429071:K9E	ENSP00000274542:K23E	K	-	1	0	RNF145	158563221	0.001000	0.12720	0.000000	0.03702	0.003000	0.03518	0.077000	0.14738	0.083000	0.17047	0.397000	0.26171	AAG	.	.	none		0.363	RNF145-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374048.1	NM_144726	
FBLN1	2192	hgsc.bcm.edu	37	22	45937241	45937241	+	Missense_Mutation	SNP	C	C	T	rs540607391		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr22:45937241C>T	ENST00000327858.6	+	9	1150	c.1055C>T	c.(1054-1056)aCg>aTg	p.T352M	FBLN1_ENST00000442170.2_Missense_Mutation_p.T352M|FBLN1_ENST00000348697.2_Missense_Mutation_p.T352M|FBLN1_ENST00000402984.3_Missense_Mutation_p.T390M|FBLN1_ENST00000476366.1_3'UTR|FBLN1_ENST00000340923.5_Missense_Mutation_p.T352M|FBLN1_ENST00000262722.7_Missense_Mutation_p.T352M	NM_006486.2	NP_006477	P23142	FBLN1_HUMAN	fibulin 1	352	EGF-like 4; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				embryo implantation (GO:0007566)|extracellular matrix organization (GO:0030198)|viral process (GO:0016032)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)|peptidase activator activity (GO:0016504)			biliary_tract(1)|central_nervous_system(1)|endometrium(4)|kidney(5)|large_intestine(7)|lung(8)|ovary(2)|prostate(1)|skin(1)	30		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0182)		GAGGAGGGAACGCGCTGTGTT	0.522													C|||	1	0.000199681	0.0008	0.0	5008	,	,		20118	0.0		0.0	False		,,,				2504	0.0				p.T352M		Atlas-SNP	.											.	FBLN1	143	.	0			c.C1055T						PASS	.						101.0	84.0	89.0					22																	45937241		2203	4300	6503	SO:0001583	missense	2192	exon9			AGGGAACGCGCTG		CCDS14067.1, CCDS14068.1, CCDS14069.1, CCDS43028.1	22q13.31	2010-06-15			ENSG00000077942	ENSG00000077942		"""Fibulins"""	3600	protein-coding gene	gene with protein product		135820				2269669, 1400330	Standard	NM_006485		Approved	FBLN	uc003bgj.1	P23142	OTTHUMG00000151340	ENST00000327858.6:c.1055C>T	22.37:g.45937241C>T	ENSP00000331544:p.Thr352Met	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	83	28	0.337349	NM_006487	B0QY42|B1AHL4|P23143|P23144|P37888|Q5TIC4|Q8TBH8|Q9HBQ5|Q9UC21|Q9UGR4|Q9UH41	Missense_Mutation	SNP	ENST00000327858.6	37	CCDS14067.1	.	.	.	.	.	.	.	.	.	.	C	16.34	3.097040	0.56075	.	.	ENSG00000077942	ENST00000348697;ENST00000402984;ENST00000262722;ENST00000327858;ENST00000442170;ENST00000340923	D;D;D;D;D;D	0.92858	-3.12;-3.12;-3.12;-2.28;-3.12;-3.12	5.41	3.26	0.37387	EGF-like calcium-binding (2);	0.150392	0.64402	D	0.000014	D	0.93458	0.7913	L	0.45285	1.41	0.09310	N	0.99999	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.85130	0.997;0.995;0.991;0.995	D	0.87244	0.2268	10	0.66056	D	0.02	.	11.9956	0.53201	0.1373:0.7308:0.1319:0.0	.	390;352;352;352	B1AHL2;P23142;B1AHL4;P23142-4	.;FBLN1_HUMAN;.;.	M	352;390;352;352;352;352	ENSP00000262723:T352M;ENSP00000385521:T390M;ENSP00000262722:T352M;ENSP00000331544:T352M;ENSP00000393812:T352M;ENSP00000342212:T352M	ENSP00000262722:T352M	T	+	2	0	FBLN1	44315905	0.909000	0.30893	0.017000	0.16124	0.824000	0.46624	1.899000	0.39818	0.627000	0.30340	0.655000	0.94253	ACG	.	.	none		0.522	FBLN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000322287.1	NM_006486	
ZNF502	91392	hgsc.bcm.edu	37	3	44762830	44762830	+	Missense_Mutation	SNP	A	A	G	rs56084453	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr3:44762830A>G	ENST00000296091.4	+	4	777	c.521A>G	c.(520-522)cAg>cGg	p.Q174R	ZNF502_ENST00000449836.1_Missense_Mutation_p.Q174R|ZNF502_ENST00000436624.2_Missense_Mutation_p.Q174R	NM_001134440.1|NM_001282880.1|NM_033210.4	NP_001127912.1|NP_001269809.1|NP_149987.2	Q8TBZ5	ZN502_HUMAN	zinc finger protein 502	174			Q -> R (in dbSNP:rs56084453).		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(4)|large_intestine(8)|lung(4)|prostate(1)|urinary_tract(1)	19				BRCA - Breast invasive adenocarcinoma(193;0.00855)|KIRC - Kidney renal clear cell carcinoma(197;0.0471)|Kidney(197;0.0589)		ACCCAACATCAGAGAACTCAT	0.408													A|||	531	0.10603	0.0129	0.1571	5008	,	,		21464	0.0446		0.2247	False		,,,				2504	0.137				p.Q174R		Atlas-SNP	.											ZNF502,NS,carcinoma,-1,1	ZNF502	58	1	0			c.A521G						PASS	.	A	ARG/GLN,ARG/GLN,ARG/GLN,ARG/GLN	190,4216	119.6+/-157.3	5,180,2018	126.0	137.0	133.0		521,521,521,521	4.7	1.0	3	dbSNP_129	133	1862,6738	329.3+/-318.7	195,1472,2633	yes	missense,missense,missense,missense	ZNF502	NM_001134440.1,NM_001134441.1,NM_001134442.1,NM_033210.4	43,43,43,43	200,1652,4651	GG,GA,AA		21.6512,4.3123,15.7773	benign,benign,benign,benign	174/545,174/545,174/545,174/545	44762830	2052,10954	2203	4300	6503	SO:0001583	missense	91392	exon4			AACATCAGAGAAC	AK022577	CCDS2719.1	3p21.32	2013-01-08			ENSG00000196653	ENSG00000196653		"""Zinc fingers, C2H2-type"""	23718	protein-coding gene	gene with protein product							Standard	NM_033210		Approved	FLJ14855, FLJ12515	uc003cnt.3	Q8TBZ5	OTTHUMG00000133086	ENST00000296091.4:c.521A>G	3.37:g.44762830A>G	ENSP00000296091:p.Gln174Arg	Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	202	10	0.049505	NM_001134440		Missense_Mutation	SNP	ENST00000296091.4	37	CCDS2719.1	282	0.12912087912087913	10	0.02032520325203252	73	0.20165745856353592	29	0.050699300699300696	170	0.22427440633245382	A	15.35	2.807929	0.50421	0.043123	0.216512	ENSG00000196653	ENST00000449836;ENST00000296091;ENST00000436624;ENST00000427783	T;T;T	0.07327	3.2;3.2;3.2	4.7	4.7	0.59300	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.16098	0.37	0.37027	P	0.103526	P	0.52463	0.953	P	0.47864	0.559	T	0.52305	-0.8593	8	0.54805	T	0.06	-5.6043	13.5531	0.61745	1.0:0.0:0.0:0.0	rs56084453;rs61740962	174	Q8TBZ5	ZN502_HUMAN	R	174	ENSP00000397390:Q174R;ENSP00000296091:Q174R;ENSP00000406469:Q174R	ENSP00000296091:Q174R	Q	+	2	0	ZNF502	44737834	0.049000	0.20398	0.972000	0.41901	0.997000	0.91878	0.860000	0.27871	2.109000	0.64355	0.533000	0.62120	CAG	A|0.848;G|0.152	0.152	strong		0.408	ZNF502-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256744.4	NM_033210	
TAF1L	138474	hgsc.bcm.edu	37	9	32631369	32631369	+	Silent	SNP	C	C	T	rs10971047	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr9:32631369C>T	ENST00000242310.4	-	1	4298	c.4209G>A	c.(4207-4209)acG>acA	p.T1403T	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	1403					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)		TGGATGACAGCGTCACCATAG	0.458													C|||	809	0.161542	0.1097	0.1182	5008	,	,		21985	0.3095		0.1034	False		,,,				2504	0.1697				p.T1403T		Atlas-SNP	.											TAF1L,NS,carcinoma,-1,1	TAF1L	382	1	0			c.G4209A						scavenged	.	C		374,4032	188.5+/-214.9	13,348,1842	297.0	272.0	280.0		4209	-0.9	0.9	9	dbSNP_120	280	893,7707	201.1+/-244.7	44,805,3451	no	coding-synonymous	TAF1L	NM_153809.2		57,1153,5293	TT,TC,CC		10.3837,8.4884,9.7417		1403/1827	32631369	1267,11739	2203	4300	6503	SO:0001819	synonymous_variant	138474	exon1			TGACAGCGTCACC	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.4209G>A	9.37:g.32631369C>T		Somatic	241	2	0.00829876		WXS	Illumina HiSeq	Phase_I	229	11	0.0480349	NM_153809	Q0VG57	Silent	SNP	ENST00000242310.4	37	CCDS35003.1																																																																																			C|0.873;T|0.127	0.127	strong		0.458	TAF1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052012.2		
ARHGEF5	7984	hgsc.bcm.edu	37	7	144060802	144060802	+	Missense_Mutation	SNP	C	C	T	rs3823677		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr7:144060802C>T	ENST00000056217.5	+	2	1214	c.1040C>T	c.(1039-1041)aCc>aTc	p.T347I	ARHGEF5_ENST00000471847.2_5'Flank	NM_005435.3	NP_005426.2	Q12774	ARHG5_HUMAN	Rho guanine nucleotide exchange factor (GEF) 5	347					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)			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)					AAGAGTCAAACCTTTTTGGGA	0.527																																					p.T347I		Atlas-SNP	.											ARHGEF5,colon,carcinoma,+1,1	ARHGEF5	73	1	0			c.C1040T						scavenged	.						62.0	56.0	58.0					7																	144060802		2079	3981	6060	SO:0001583	missense	7984	exon2			GTCAAACCTTTTT	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.1040C>T	7.37:g.144060802C>T	ENSP00000056217:p.Thr347Ile	Somatic	269	1	0.00371747		WXS	Illumina HiSeq	Phase_I	266	12	0.0451128	NM_005435	A6NNJ2|Q6ZML7	Missense_Mutation	SNP	ENST00000056217.5	37	CCDS34771.1	764	0.3498168498168498	142	0.2886178861788618	126	0.34806629834254144	284	0.4965034965034965	212	0.2796833773087071	c	8.471	0.857559	0.17106	.	.	ENSG00000050327	ENST00000056217	T	0.73047	-0.71	3.54	-2.18	0.07037	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.06786	0.001	B	0.08055	0.003	T	0.44802	-0.9304	7	.	.	.	-0.3178	0.5401	0.00644	0.2016:0.2872:0.2203:0.2909	.	347	Q12774	ARHG5_HUMAN	I	347	ENSP00000056217:T347I	.	T	+	2	0	ARHGEF5	143691735	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.478000	0.06575	-0.083000	0.12618	-0.235000	0.12190	ACC	.	.	weak		0.527	ARHGEF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349981.1	NM_005435	
EP300	2033	hgsc.bcm.edu	37	22	41551039	41551039	+	Silent	SNP	T	T	A	rs20552	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr22:41551039T>A	ENST00000263253.7	+	17	4402	c.3183T>A	c.(3181-3183)acT>acA	p.T1061T		NM_001429.3	NP_001420.2	Q09472	EP300_HUMAN	E1A binding protein p300	1061					apoptotic process (GO:0006915)|cellular response to hypoxia (GO:0071456)|chromatin organization (GO:0006325)|circadian rhythm (GO:0007623)|G2/M transition of mitotic cell cycle (GO:0000086)|heart development (GO:0007507)|histone H2B acetylation (GO:0043969)|histone H4 acetylation (GO:0043967)|innate immune response (GO:0045087)|internal peptidyl-lysine acetylation (GO:0018393)|internal protein amino acid acetylation (GO:0006475)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|lung development (GO:0030324)|mitotic cell cycle (GO:0000278)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of protein binding (GO:0032092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of cell cycle (GO:0051726)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)|regulation of tubulin deacetylation (GO:0090043)|response to estrogen (GO:0043627)|response to hypoxia (GO:0001666)|skeletal muscle tissue development (GO:0007519)|somitogenesis (GO:0001756)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	acetyltransferase activity (GO:0016407)|activating transcription factor binding (GO:0033613)|androgen receptor binding (GO:0050681)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|lysine N-acetyltransferase activity, acting on acetyl phosphate as donor (GO:0004468)|nuclear hormone receptor binding (GO:0035257)|pre-mRNA intronic binding (GO:0097157)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transferase activity, transferring acyl groups (GO:0016746)|zinc ion binding (GO:0008270)			NS(2)|breast(11)|central_nervous_system(7)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(31)|kidney(5)|large_intestine(31)|liver(2)|lung(33)|ovary(2)|pancreas(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(16)	171						TGATGCCAACTTTGGAGGCAC	0.388			"""T,  N, F, Mis, O"""	"""MLL, RUNXBP2"""	"""colorectal, breast, pancreatic, AML, ALL, DLBCL"""				Rubinstein-Taybi syndrome				A|||	3375	0.673922	0.5091	0.7695	5008	,	,		17967	0.8175		0.6352	False		,,,				2504	0.7209				p.T1061T		Atlas-SNP	.		Rec	yes		22	22q13	2033	300 kd E1A-Binding protein gene		"""L, E"""	.	EP300	367	.	0			c.T3183A						PASS	.	A		2246,2160	582.1+/-385.5	583,1080,540	214.0	200.0	205.0		3183	-2.4	0.2	22	dbSNP_67	205	5338,3262	490.3+/-372.8	1690,1958,652	no	coding-synonymous	EP300	NM_001429.3		2273,3038,1192	AA,AT,TT		37.9302,49.0241,41.6885		1061/2415	41551039	7584,5422	2203	4300	6503	SO:0001819	synonymous_variant	2033	exon17	Familial Cancer Database	Broad Thumb-Hallux syndrome	GCCAACTTTGGAG	U01877	CCDS14010.1	22q13.2	2011-07-01			ENSG00000100393	ENSG00000100393		"""Chromatin-modifying enzymes / K-acetyltransferases"""	3373	protein-coding gene	gene with protein product	"""histone acetyltransferase p300"""	602700				7523245	Standard	NM_001429		Approved	p300, KAT3B	uc003azl.4	Q09472	OTTHUMG00000150937	ENST00000263253.7:c.3183T>A	22.37:g.41551039T>A		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	117	5	0.042735	NM_001429	B1AKC2	Silent	SNP	ENST00000263253.7	37	CCDS14010.1																																																																																			T|0.375;A|0.625	0.625	strong		0.388	EP300-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320600.1	NM_001429	
PLEKHA3	65977	hgsc.bcm.edu	37	2	179358665	179358665	+	Silent	SNP	A	A	G	rs2303536	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr2:179358665A>G	ENST00000234453.5	+	4	801	c.399A>G	c.(397-399)acA>acG	p.T133T	PLEKHA3_ENST00000461474.1_3'UTR	NM_019091.3	NP_061964.3	Q9HB20	PKHA3_HUMAN	pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 3	133						Golgi apparatus (GO:0005794)|membrane (GO:0016020)	1-phosphatidylinositol binding (GO:0005545)|phospholipid binding (GO:0005543)			endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)	11			OV - Ovarian serous cystadenocarcinoma(117;0.0112)|Epithelial(96;0.0266)|all cancers(119;0.0865)			AAGTTCATACAATACAGGAAT	0.403													G|||	1527	0.304912	0.2095	0.1945	5008	,	,		20258	0.63		0.1551	False		,,,				2504	0.3313				p.T133T		Atlas-SNP	.											PLEKHA3,NS,carcinoma,+1,1	PLEKHA3	25	1	0			c.A399G						scavenged	.	G		883,3523	741.1+/-411.2	90,703,1410	126.0	118.0	120.0		399	-11.7	0.4	2	dbSNP_100	120	1271,7329	760.0+/-407.6	99,1073,3128	no	coding-synonymous	PLEKHA3	NM_019091.3		189,1776,4538	GG,GA,AA		14.7791,20.0409,16.5616		133/301	179358665	2154,10852	2203	4300	6503	SO:0001819	synonymous_variant	65977	exon4			TCATACAATACAG	AF286162	CCDS33336.1	2q31.2	2013-01-10	2002-01-14		ENSG00000116095	ENSG00000116095		"""Pleckstrin homology (PH) domain containing"""	14338	protein-coding gene	gene with protein product	"""four-phosphate-adaptor protein 1"""	607774	"""pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 3"""			11001876, 15107860	Standard	NM_019091		Approved	FAPP1	uc002umn.3	Q9HB20	OTTHUMG00000154446	ENST00000234453.5:c.399A>G	2.37:g.179358665A>G		Somatic	243	0	0		WXS	Illumina HiSeq	Phase_I	194	3	0.0154639	NM_019091	Q4ZG69|Q86TQ1|Q9NXT3	Silent	SNP	ENST00000234453.5	37	CCDS33336.1																																																																																			A|1.000;|0.000	.	weak		0.403	PLEKHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335241.2	NM_019091	
ARID1A	8289	hgsc.bcm.edu	37	1	27102083	27102083	+	Nonsense_Mutation	SNP	G	G	A			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr1:27102083G>A	ENST00000324856.7	+	19	5380	c.5009G>A	c.(5008-5010)tGg>tAg	p.W1670*	ARID1A_ENST00000457599.2_Nonsense_Mutation_p.W1453*|ARID1A_ENST00000374152.2_Nonsense_Mutation_p.W1287*|ARID1A_ENST00000540690.1_5'UTR	NM_006015.4	NP_006006.3	O14497	ARI1A_HUMAN	AT rich interactive domain 1A (SWI-like)	1670					androgen receptor signaling pathway (GO:0030521)|ATP-dependent chromatin remodeling (GO:0043044)|cardiac chamber development (GO:0003205)|chromatin remodeling (GO:0006338)|chromatin-mediated maintenance of transcription (GO:0048096)|forebrain development (GO:0030900)|glucocorticoid receptor signaling pathway (GO:0042921)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|nucleosome disassembly (GO:0006337)|nucleosome mobilization (GO:0042766)|optic cup formation involved in camera-type eye development (GO:0003408)|placenta blood vessel development (GO:0060674)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|transcription coactivator activity (GO:0003713)	p.W1670*(1)	ARID1A/MAST2_ENST00000361297(2)	NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(13)|central_nervous_system(6)|cervix(2)|endometrium(56)|haematopoietic_and_lymphoid_tissue(8)|kidney(10)|large_intestine(41)|liver(31)|lung(34)|ovary(130)|pancreas(18)|prostate(8)|skin(9)|stomach(14)|upper_aerodigestive_tract(4)|urinary_tract(24)	411		all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242)		CCGGAGGCATGGCGGGTAATG	0.542			"""Mis, N, F, S, D"""		"""clear cell ovarian carcinoma, RCC"""																																p.W1670X		Atlas-SNP	.		Rec	yes		1	1p35.3	8289	AT rich interactive domain 1A (SWI-like)		E	ARID1A,bladder,carcinoma,0,1	ARID1A	842	1	1	Substitution - Nonsense(1)	urinary_tract(1)	c.G5009A						PASS	.						80.0	67.0	71.0					1																	27102083		2203	4300	6503	SO:0001587	stop_gained	8289	exon19			AGGCATGGCGGGT	AB001895	CCDS285.1, CCDS44091.1	1p36.1-p35	2014-09-17	2006-11-08	2004-01-30	ENSG00000117713	ENSG00000117713		"""-"""	11110	protein-coding gene	gene with protein product		603024	"""SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily f, member 1"", ""AT rich interactive domain 1A (SWI- like)"""	C1orf4, SMARCF1		9630625, 9434167	Standard	NM_139135		Approved	B120, P270, C10rf4, BAF250, BAF250a	uc001bmv.1	O14497	OTTHUMG00000004004	ENST00000324856.7:c.5009G>A	1.37:g.27102083G>A	ENSP00000320485:p.Trp1670*	Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	43	17	0.395349	NM_006015	D3DPL1|Q53FK9|Q5T0W1|Q5T0W2|Q5T0W3|Q8NFD6|Q96T89|Q9BY33|Q9HBJ5|Q9UPZ1	Nonsense_Mutation	SNP	ENST00000324856.7	37	CCDS285.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	44|44	10.783098|10.783098	0.99467|0.99467	.|.	.|.	ENSG00000117713|ENSG00000117713	ENST00000430799|ENST00000324856;ENST00000457599;ENST00000374152	.|.	.|.	.|.	5.05|5.05	5.05|5.05	0.67936|0.67936	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|.	0.46560|.	0.1399|.	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.34825|.	-0.9813|.	4|.	.|0.02654	.|T	.|1	-4.3496|-4.3496	18.5907|18.5907	0.91210|0.91210	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|.	.|.	.|.	I|X	566|1670;1453;1287	.|.	.|ENSP00000320485:W1670X	M|W	+|+	3|2	0|0	ARID1A|ARID1A	26974670|26974670	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	9.657000|9.657000	0.98554|0.98554	2.634000|2.634000	0.89283|0.89283	0.655000|0.655000	0.94253|0.94253	ATG|TGG	.	.	none		0.542	ARID1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011437.2	NM_139135	
NNT	23530	hgsc.bcm.edu	37	5	43613046	43613046	+	Missense_Mutation	SNP	A	A	G	rs35201656	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr5:43613046A>G	ENST00000264663.5	+	3	409	c.188A>G	c.(187-189)aAa>aGa	p.K63R	NNT_ENST00000344920.4_Missense_Mutation_p.K63R|NNT_ENST00000512996.2_5'UTR	NM_012343.3	NP_036475.3	Q13423	NNTM_HUMAN	nicotinamide nucleotide transhydrogenase	63					cellular metabolic process (GO:0044237)|hydrogen ion transmembrane transport (GO:1902600)|oxidation-reduction process (GO:0055114)|proton transport (GO:0015992)|reactive oxygen species metabolic process (GO:0072593)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain (GO:0005746)|mitochondrion (GO:0005739)	NAD binding (GO:0051287)|NAD(P)+ transhydrogenase (AB-specific) activity (GO:0008750)|NAD(P)+ transhydrogenase (B-specific) activity (GO:0003957)|NAD(P)+ transhydrogenase activity (GO:0008746)|NADP binding (GO:0050661)	p.K63R(1)		breast(1)|central_nervous_system(2)|endometrium(2)|kidney(7)|large_intestine(6)|liver(2)|lung(20)|ovary(3)|prostate(2)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	Lung NSC(6;2.58e-06)					GGAGTCCCCAAAGAGATATTC	0.388													A|||	212	0.0423323	0.0015	0.0216	5008	,	,		17260	0.1062		0.0378	False		,,,				2504	0.0511				p.K63R		Atlas-SNP	.											NNT,NS,carcinoma,0,1	NNT	92	1	1	Substitution - Missense(1)	stomach(1)	c.A188G						scavenged	.	A	ARG/LYS,ARG/LYS	44,4362	47.5+/-82.1	1,42,2160	125.0	131.0	129.0		188,188	2.0	1.0	5	dbSNP_126	129	361,8239	120.1+/-179.3	5,351,3944	yes	missense,missense	NNT	NM_012343.3,NM_182977.2	26,26	6,393,6104	GG,GA,AA		4.1977,0.9986,3.1139	benign,benign	63/1087,63/1087	43613046	405,12601	2203	4300	6503	SO:0001583	missense	23530	exon3			TCCCCAAAGAGAT	U40490	CCDS3949.1	5p12	2008-02-05			ENSG00000112992	ENSG00000112992	1.6.1.1		7863	protein-coding gene	gene with protein product		607878				9271681, 9524818	Standard	NM_182977		Approved		uc003jof.3	Q13423	OTTHUMG00000096961	ENST00000264663.5:c.188A>G	5.37:g.43613046A>G	ENSP00000264663:p.Lys63Arg	Somatic	172	1	0.00581395		WXS	Illumina HiSeq	Phase_I	221	5	0.0226244	NM_182977	Q16796|Q2TB60|Q8N3V4	Missense_Mutation	SNP	ENST00000264663.5	37	CCDS3949.1	93	0.042582417582417584	1	0.0020325203252032522	7	0.019337016574585635	55	0.09615384615384616	30	0.0395778364116095	A	16.84	3.234226	0.58886	0.009986	0.041977	ENSG00000112992	ENST00000505678;ENST00000512422;ENST00000264663;ENST00000344920	T;T;T;T	0.78246	-1.16;-1.16;-1.16;-1.16	5.7	1.95	0.26073	Alanine dehydrogenase/pyridine nucleotide transhydrogenase, conserved site-1 (1);Alanine dehydrogenase/PNT, N-terminal (1);	0.087586	0.85682	N	0.000000	T	0.06645	0.0170	L	0.35593	1.075	0.80722	D	1	P	0.47409	0.895	P	0.52881	0.712	T	0.12993	-1.0526	10	0.20046	T	0.44	-7.2108	9.8845	0.41253	0.805:0.0:0.195:0.0	rs35201656	63	Q13423	NNTM_HUMAN	R	63	ENSP00000427670:K63R;ENSP00000421886:K63R;ENSP00000264663:K63R;ENSP00000343873:K63R	ENSP00000264663:K63R	K	+	2	0	NNT	43648803	1.000000	0.71417	0.998000	0.56505	0.977000	0.68977	4.327000	0.59247	0.101000	0.17610	-0.274000	0.10170	AAA	A|0.964;G|0.036	0.036	strong		0.388	NNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214026.1	NM_182977	
ADAM28	10863	hgsc.bcm.edu	37	8	24171051	24171051	+	Silent	SNP	C	C	T	rs6996616	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr8:24171051C>T	ENST00000265769.4	+	6	644	c.534C>T	c.(532-534)caC>caT	p.H178H	RP11-624C23.1_ENST00000523700.1_RNA|ADAM28_ENST00000540823.1_Intron|RP11-624C23.1_ENST00000519689.1_RNA|RP11-624C23.1_ENST00000518988.1_RNA|ADAM28_ENST00000437154.2_Silent_p.H178H|RP11-624C23.1_ENST00000523578.1_RNA|ADAM28_ENST00000397649.3_5'UTR	NM_014265.4	NP_055080.2	Q9UKQ2	ADA28_HUMAN	ADAM metallopeptidase domain 28	178					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)		TGTGGGCCCACGATTTGCAGC	0.448													T|||	932	0.186102	0.152	0.0965	5008	,	,		16774	0.3621		0.1571	False		,,,				2504	0.1442				p.H178H	NSCLC(193;488 2149 22258 34798 40734)	Atlas-SNP	.											.	ADAM28	100	.	0			c.C534T						PASS	.	T	,	754,3652	755.8+/-412.6	65,624,1514	208.0	181.0	190.0		534,534	0.0	0.0	8	dbSNP_116	190	1315,7285	758.0+/-407.5	104,1107,3089	no	coding-synonymous,coding-synonymous	ADAM28	NM_014265.4,NM_021777.3	,	169,1731,4603	TT,TC,CC		15.2907,17.113,15.908	,	178/776,178/541	24171051	2069,10937	2203	4300	6503	SO:0001819	synonymous_variant	10863	exon6			GGCCCACGATTTG	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.534C>T	8.37:g.24171051C>T		Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	182	8	0.043956	NM_014265	B2RMV5|Q9Y339|Q9Y3S0	Silent	SNP	ENST00000265769.4	37	CCDS34865.1																																																																																			C|0.809;T|0.191	0.191	strong		0.448	ADAM28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375441.2	NM_021778	
MAP9	79884	hgsc.bcm.edu	37	4	156274377	156274377	+	Missense_Mutation	SNP	T	T	C	rs1058992	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr4:156274377T>C	ENST00000311277.4	-	11	1759	c.1496A>G	c.(1495-1497)aAg>aGg	p.K499R	AC097467.2_ENST00000601977.1_RNA|AC097467.2_ENST00000609486.1_RNA|AC097467.2_ENST00000610249.1_RNA|MAP9_ENST00000515654.1_Missense_Mutation_p.K475R|AC097467.2_ENST00000608762.1_RNA|AC097467.2_ENST00000595229.1_RNA|AC097467.2_ENST00000597939.1_RNA|AC097467.2_ENST00000417474.1_RNA|AC097467.2_ENST00000593387.2_RNA|AC097467.2_ENST00000609254.1_RNA|AC097467.2_ENST00000608544.1_RNA|AC097467.2_ENST00000609716.1_RNA|AC097467.2_ENST00000608092.1_RNA|AC097467.2_ENST00000608406.1_RNA|AC097467.2_ENST00000608463.1_RNA|AC097467.2_ENST00000599555.2_RNA|AC097467.2_ENST00000598252.1_RNA	NM_001039580.1	NP_001034669.1	Q49MG5	MAP9_HUMAN	microtubule-associated protein 9	499			K -> R (in dbSNP:rs1058992).		cytokinesis (GO:0000910)|regulation of mitosis (GO:0007088)|spindle assembly involved in mitosis (GO:0090307)	astral microtubule (GO:0000235)|mitotic spindle midzone (GO:1990023)		p.K499R(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(8)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	26	all_hematologic(180;0.24)	Renal(120;0.0458)		COAD - Colon adenocarcinoma(41;0.143)		TTCAGTTTTCTTCTTGTTTTT	0.333													T|||	2048	0.408946	0.6104	0.3228	5008	,	,		14025	0.5863		0.2247	False		,,,				2504	0.2045				p.K499R		Atlas-SNP	.											MAP9,NS,carcinoma,0,1	MAP9	79	1	1	Substitution - Missense(1)	prostate(1)	c.A1496G						PASS	.	T	ARG/LYS	2319,2085	603.3+/-390.1	631,1057,514	108.0	104.0	106.0		1496	4.1	1.0	4	dbSNP_86	106	1857,6739	332.3+/-320.0	193,1471,2634	yes	missense	MAP9	NM_001039580.1	26	824,2528,3148	CC,CT,TT		21.6031,47.3433,32.1231	probably-damaging	499/648	156274377	4176,8824	2202	4298	6500	SO:0001583	missense	79884	exon11			GTTTTCTTCTTGT	AK024812	CCDS35493.1	4q32.1	2008-02-05			ENSG00000164114	ENSG00000164114			26118	protein-coding gene	gene with protein product	"""aster-associated protein"""	610070				16049101	Standard	XM_006714306		Approved	ASAP, FLJ21159	uc003ios.3	Q49MG5	OTTHUMG00000133628	ENST00000311277.4:c.1496A>G	4.37:g.156274377T>C	ENSP00000310593:p.Lys499Arg	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	68	4	0.0588235	NM_001039580	Q4W5I7|Q68DU1|Q9H781|Q9H7B6	Missense_Mutation	SNP	ENST00000311277.4	37	CCDS35493.1	921	0.4217032967032967	307	0.6239837398373984	104	0.287292817679558	329	0.5751748251748252	181	0.23878627968337732	T	10.92	1.487296	0.26686	0.526567	0.216031	ENSG00000164114	ENST00000311277;ENST00000515654	T;T	0.09445	2.98;2.98	5.23	4.05	0.47172	.	0.402707	0.28700	N	0.014428	T	0.00012	0.0000	M	0.69823	2.125	0.09310	P	0.9999999999743422	B;B;B	0.32203	0.169;0.36;0.169	B;B;B	0.32022	0.091;0.139;0.091	T	0.19321	-1.0309	9	0.19147	T	0.46	-13.891	8.6845	0.34229	0.0:0.0879:0.0:0.9121	rs17357030	474;499;499	B4DVG9;B9EJB6;Q49MG5	.;.;MAP9_HUMAN	R	499;475	ENSP00000310593:K499R;ENSP00000427402:K475R	ENSP00000310593:K499R	K	-	2	0	MAP9	156493827	0.914000	0.31030	1.000000	0.80357	0.991000	0.79684	0.012000	0.13287	0.930000	0.37217	0.533000	0.62120	AAG	T|0.652;C|0.348	0.348	strong		0.333	MAP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257771.3	NM_001039580	
DND1	373863	hgsc.bcm.edu	37	5	140050894	140050894	+	Missense_Mutation	SNP	G	G	C	rs201638404		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr5:140050894G>C	ENST00000542735.1	-	4	1089	c.1046C>G	c.(1045-1047)aCc>aGc	p.T349S	WDR55_ENST00000358337.5_3'UTR|WDR55_ENST00000520764.1_3'UTR	NM_194249.2	NP_919225.1	Q8IYX4	DND1_HUMAN	DND microRNA-mediated repression inhibitor 1	349					germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|negative regulation of gene silencing by miRNA (GO:0060965)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	AU-rich element binding (GO:0017091)|nucleotide binding (GO:0000166)			central_nervous_system(1)|prostate(4)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TTTAACCATGGTACCTGCCTC	0.602																																					p.T349S		Atlas-SNP	.											DND1,NS,carcinoma,-1,1	DND1	15	1	0			c.C1046G						scavenged	.						75.0	61.0	66.0					5																	140050894		1959	3964	5923	SO:0001583	missense	373863	exon4			ACCATGGTACCTG	AY321065	CCDS4236.1	5q31.3	2013-07-31	2013-07-31		ENSG00000256453	ENSG00000256453		"""RNA binding motif (RRM) containing"""	23799	protein-coding gene	gene with protein product		609385	"""dead end homolog 1 (zebrafish)"""			12932328	Standard	NM_194249		Approved	MGC34750, RBMS4	uc003lgt.3	Q8IYX4	OTTHUMG00000129499	ENST00000542735.1:c.1046C>G	5.37:g.140050894G>C	ENSP00000445366:p.Thr349Ser	Somatic	313	7	0.0223642		WXS	Illumina HiSeq	Phase_I	313	13	0.0415335	NM_194249		Missense_Mutation	SNP	ENST00000542735.1	37	CCDS4236.1	.	.	.	.	.	.	.	.	.	.	G	9.262	1.043394	0.19748	.	.	ENSG00000256453	ENST00000542735	T	0.30182	1.54	4.97	0.117	0.14652	.	1.006470	0.07994	N	0.987573	T	0.16769	0.0403	N	0.19112	0.55	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.29518	-1.0009	10	0.27082	T	0.32	0.0017	3.9136	0.09213	0.3271:0.0:0.5115:0.1614	.	349	Q8IYX4	DND1_HUMAN	S	349	ENSP00000445366:T349S	ENSP00000445366:T349S	T	-	2	0	DND1	140031078	0.002000	0.14202	0.000000	0.03702	0.312000	0.27988	0.583000	0.23849	0.101000	0.17610	0.551000	0.68910	ACC	G|0.979;C|0.021	0.021	strong		0.602	DND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251669.2	NM_194249	
MARCH1	55016	hgsc.bcm.edu	37	4	165118819	165118819	+	Intron	SNP	C	C	T			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr4:165118819C>T	ENST00000503008.1	-	2	864				MARCH1_ENST00000508725.1_Intron|MARCH1_ENST00000514618.1_Intron	NM_001166373.1	NP_001159845.1	Q8TCQ1	MARH1_HUMAN	membrane-associated ring finger (C3HC4) 1, E3 ubiquitin protein ligase						antigen processing and presentation of peptide antigen via MHC class II (GO:0002495)|immune response (GO:0006955)|protein polyubiquitination (GO:0000209)	cytoplasmic vesicle (GO:0031410)|early endosome membrane (GO:0031901)|endoplasmic reticulum membrane (GO:0005789)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)	ligase activity (GO:0016874)|MHC protein binding (GO:0042287)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.A15A(1)		endometrium(2)|kidney(3)|large_intestine(3)|lung(20)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	36	all_hematologic(180;0.166)	Prostate(90;0.0959)|all_neural(102;0.223)				CATCAGAGGGCGCCCTGTTCC	0.502																																					p.A15A		Atlas-SNP	.											ANP32C,NS,carcinoma,0,1	ANP32C	59	1	1	Substitution - coding silent(1)	endometrium(1)	c.G45A						PASS	.						121.0	123.0	123.0					4																	165118819		2203	4300	6503	SO:0001627	intron_variant	23520	exon1			AGAGGGCGCCCTG	AK000675	CCDS3806.1, CCDS54814.1	4q32.2	2013-01-09	2012-02-23			ENSG00000145416		"""MARCH membrane-associated ring fingers"", ""RING-type (C3HC4) zinc fingers"""	26077	protein-coding gene	gene with protein product		613331	"""membrane-associated ring finger (C3HC4) 1"""			14722266	Standard	NM_017923		Approved	FLJ20668, MARCH-I, RNF171	uc003iqs.2	Q8TCQ1		ENST00000503008.1:c.113-86005G>A	4.37:g.165118819C>T		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	102	34	0.333333	NM_012403	D3DP29|Q9NWR0	Silent	SNP	ENST00000503008.1	37	CCDS54814.1																																																																																			.	.	none		0.502	MARCH1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364493.2	NM_017923	
MRGPRX4	117196	hgsc.bcm.edu	37	11	18194964	18194964	+	Missense_Mutation	SNP	A	A	G	rs1869788	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr11:18194964A>G	ENST00000314254.3	+	1	581	c.161A>G	c.(160-162)tAc>tGc	p.Y54C	RP11-113D6.6_ENST00000527671.1_Intron	NM_054032.3	NP_473373.2	Q96LA9	MRGX4_HUMAN	MAS-related GPR, member X4	54			Y -> C (in dbSNP:rs1869788). {ECO:0000269|PubMed:11850634}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(18)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	32						CTCCTGGGCTACCGCATGCGC	0.552													G|||	1845	0.368411	0.3873	0.3559	5008	,	,		21075	0.4415		0.3072	False		,,,				2504	0.3395				p.Y54C		Atlas-SNP	.											.	MRGPRX4	68	.	0			c.A161G						PASS	.	G	CYS/TYR	1625,2773		297,1031,871	129.0	114.0	119.0		161	0.4	0.0	11	dbSNP_92	119	2463,6123		346,1771,2176	no	missense	MRGPRX4	NM_054032.3	194	643,2802,3047	GG,GA,AA		28.6862,36.9486,31.4849	benign	54/323	18194964	4088,8896	2199	4293	6492	SO:0001583	missense	117196	exon1			TGGGCTACCGCAT	AY042216	CCDS7831.1	11p15.1	2013-10-10			ENSG00000179817	ENSG00000179817		"""GPCR / Class A : Orphans"""	17617	protein-coding gene	gene with protein product		607230				11551509	Standard	NM_054032		Approved	MRGX4	uc001mnv.1	Q96LA9	OTTHUMG00000166442	ENST00000314254.3:c.161A>G	11.37:g.18194964A>G	ENSP00000314042:p.Tyr54Cys	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	128	8	0.0625	NM_054032	Q3KNU3|Q3KNU4|Q502W0|Q8TDD6|Q8TDD7	Missense_Mutation	SNP	ENST00000314254.3	37	CCDS7831.1	823	0.3768315018315018	184	0.37398373983739835	122	0.3370165745856354	275	0.4807692307692308	242	0.31926121372031663	N	5.292	0.239257	0.10023	0.369486	0.286862	ENSG00000179817	ENST00000314254	T	0.09350	2.99	2.95	0.397	0.16314	GPCR, rhodopsin-like superfamily (1);	0.275863	0.31673	N	0.007243	T	0.00012	0.0000	N	0.02721	-0.515	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.45131	-0.9282	9	0.56958	D	0.05	.	5.4252	0.16421	0.1592:0.0:0.3113:0.5295	rs1869788;rs56745486	54	Q96LA9	MRGX4_HUMAN	C	54	ENSP00000314042:Y54C	ENSP00000314042:Y54C	Y	+	2	0	MRGPRX4	18151540	0.000000	0.05858	0.001000	0.08648	0.002000	0.02628	-0.336000	0.07863	-0.398000	0.07679	-4.918000	0.00002	TAC	A|0.673;G|0.327	0.327	strong		0.552	MRGPRX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389788.1	NM_054032	
MMP27	64066	hgsc.bcm.edu	37	11	102567207	102567207	+	Missense_Mutation	SNP	T	T	A	rs1276286	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr11:102567207T>A	ENST00000260229.4	-	6	888	c.797A>T	c.(796-798)gAa>gTa	p.E266V		NM_022122.2	NP_071405.2	Q9H306	MMP27_HUMAN	matrix metallopeptidase 27	266			E -> V (in dbSNP:rs1276286). {ECO:0000269|PubMed:12975309}.		collagen catabolic process (GO:0030574)	proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(2)|lung(12)|ovary(2)|prostate(2)|skin(11)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	45	all_cancers(8;0.000843)|all_epithelial(12;0.00362)|Lung NSC(15;0.21)	all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)	Epithelial(9;0.0509)|Lung(13;0.0696)|LUSC - Lung squamous cell carcinoma(19;0.13)|all cancers(10;0.176)	BRCA - Breast invasive adenocarcinoma(274;0.0151)	Marimastat(DB00786)	CTTAGCAGGTTCCTTAGGCAG	0.413													A|||	2191	0.4375	0.1725	0.5043	5008	,	,		18588	0.629		0.4443	False		,,,				2504	0.544				p.E266V		Atlas-SNP	.											MMP27,NS,carcinoma,0,1	MMP27	84	1	0			c.A797T						PASS	.	A	VAL/GLU	1066,3340	723.7+/-409.4	113,840,1250	151.0	154.0	153.0		797	-1.3	0.0	11	dbSNP_87	153	3904,4694	606.3+/-395.1	863,2178,1258	yes	missense	MMP27	NM_022122.2	121	976,3018,2508	AA,AT,TT		45.4059,24.1943,38.219	benign	266/514	102567207	4970,8034	2203	4299	6502	SO:0001583	missense	64066	exon6			GCAGGTTCCTTAG	AF195192	CCDS8319.1	11q24	2008-07-18	2005-08-08		ENSG00000137675	ENSG00000137675			14250	protein-coding gene	gene with protein product	"""matrix metalloprotease 27"""		"""matrix metalloproteinase 27"""			10419448	Standard	NM_022122		Approved		uc001phd.1	Q9H306	OTTHUMG00000168099	ENST00000260229.4:c.797A>T	11.37:g.102567207T>A	ENSP00000260229:p.Glu266Val	Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	220	10	0.0454545	NM_022122	Q6UWK6	Missense_Mutation	SNP	ENST00000260229.4	37	CCDS8319.1	931	0.42628205128205127	84	0.17073170731707318	169	0.46685082872928174	336	0.5874125874125874	342	0.45118733509234826	A	0.065	-1.215502	0.01542	0.241943	0.454059	ENSG00000137675	ENST00000260229	T	0.14266	2.52	5.89	-1.3	0.09259	.	3.758110	0.00837	N	0.001700	T	0.00012	0.0000	N	0.02830	-0.485	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.44467	-0.9326	9	0.20046	T	0.44	.	5.2352	0.15443	0.4414:0.0:0.2808:0.2778	rs1276286;rs17800318;rs52815827;rs56490119;rs1276286	266	Q9H306	MMP27_HUMAN	V	266	ENSP00000260229:E266V	ENSP00000260229:E266V	E	-	2	0	MMP27	102072417	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.450000	0.06803	-0.348000	0.08286	-1.349000	0.01238	GAA	T|0.600;A|0.400	0.400	strong		0.413	MMP27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398128.1	NM_022122	
HLA-DQA1	3117	hgsc.bcm.edu	37	6	32609094	32609094	+	Silent	SNP	C	C	T	rs550717566	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr6:32609094C>T	ENST00000343139.5	+	2	192	c.90C>T	c.(88-90)caC>caT	p.H30H	HLA-DQA1_ENST00000395363.1_Silent_p.H30H|HLA-DQA1_ENST00000374949.2_Silent_p.H30H	NM_002122.3	NP_002113.2	P01909	DQA1_HUMAN	major histocompatibility complex, class II, DQ alpha 1	30	Alpha-1.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|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)|integral component of plasma membrane (GO:0005887)|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)			NS(1)|lung(3)|skin(1)|upper_aerodigestive_tract(1)	6						CAGCTGACCACGTTGCCTCTT	0.453													.|||	1698	0.339058	0.239	0.3991	5008	,	,		17899	0.4514		0.2684	False		,,,				2504	0.3885				p.H30H		Atlas-SNP	.											.	HLA-DQA1	52	.	0			c.C90T						PASS	.	C		922,3484		131,660,1412	145.0	125.0	132.0		90	-3.5	0.0	6	dbSNP_126	132	1916,6672		341,1234,2719	no	coding-synonymous	HLA-DQA1	NM_002122.3		472,1894,4131	TT,TC,CC		22.3102,20.926,21.8408		30/256	32609094	2838,10156	2203	4294	6497	SO:0001819	synonymous_variant	3117	exon2			TGACCACGTTGCC		CCDS4752.1	6p21.3	2013-01-11			ENSG00000196735	ENSG00000196735		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4942	protein-coding gene	gene with protein product		146880		HLA-DQA			Standard	NM_002122		Approved	CELIAC1	uc003obr.3	P01909	OTTHUMG00000031106	ENST00000343139.5:c.90C>T	6.37:g.32609094C>T		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	116	7	0.0603448	NM_002122	O19630|O19706|P01907|P01908|P04225|P04226|P05536|P79553|Q06751|Q29876|Q29994|Q2Q6Y6|Q2Q6Y7|Q2Q6Y8|Q2WCM3|Q30064|Q30067|Q30068|Q30070|Q30071|Q30072|Q30073|Q30086|Q30101|Q5Y7D5|Q5Y7F5|Q6ICU6|Q6PR46|Q6QDB1|Q860W2|Q860W4|Q9BD37|Q9TPM3|Q9UM31	Silent	SNP	ENST00000343139.5	37	CCDS4752.1	768	0.3516483516483517	114	0.23170731707317074	137	0.3784530386740331	292	0.5104895104895105	225	0.29683377308707126	.	2.853	-0.237898	0.05944	0.20926	0.223102	ENSG00000196735	ENST00000486548	.	.	.	3.84	-3.45	0.04781	.	.	.	.	.	T	0.22936	0.0554	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.22730	-1.0208	3	.	.	.	.	10.9663	0.47414	0.0:0.3747:0.0:0.6253	rs12722043;rs17415840	.	.	.	M	3	.	.	T	+	2	0	HLA-DQA1	32717072	0.000000	0.05858	0.020000	0.16555	0.047000	0.14425	-4.803000	0.00184	-0.758000	0.04690	0.462000	0.41574	ACG	C|0.706;T|0.294	0.294	strong		0.453	HLA-DQA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076176.3	NM_002122	
NLRP9	338321	hgsc.bcm.edu	37	19	56249530	56249530	+	Missense_Mutation	SNP	C	C	A			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr19:56249530C>A	ENST00000332836.2	-	1	238	c.211G>T	c.(211-213)Gta>Tta	p.V71L	RN7SKP109_ENST00000410592.1_RNA	NM_176820.2	NP_789790.2	Q7RTR0	NALP9_HUMAN	NLR family, pyrin domain containing 9	71	DAPIN. {ECO:0000255|PROSITE- ProRule:PRU00061}.					cytoplasm (GO:0005737)	ATP binding (GO:0005524)			NS(2)|breast(5)|cervix(1)|endometrium(7)|kidney(8)|large_intestine(15)|lung(21)|ovary(2)|prostate(3)|skin(7)|urinary_tract(3)	74		Colorectal(82;0.000133)|Ovarian(87;0.133)		GBM - Glioblastoma multiforme(193;0.123)		TTCAGTGTTACCTCCCATGCC	0.493																																					p.V71L		Atlas-SNP	.											.	NLRP9	163	.	0			c.G211T						PASS	.						444.0	438.0	440.0					19																	56249530		2203	4300	6503	SO:0001583	missense	338321	exon1			GTGTTACCTCCCA	AY154464	CCDS12934.1	19q13.43	2006-12-08	2006-12-08	2006-12-08				"""Nucleotide-binding domain and leucine rich repeat containing"""	22941	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 9"""	609663	"""NACHT, leucine rich repeat and PYD containing 9"""	NALP9		12563287	Standard	NM_176820		Approved	NOD6, PAN12, CLR19.1	uc002qly.3	Q7RTR0		ENST00000332836.2:c.211G>T	19.37:g.56249530C>A	ENSP00000331857:p.Val71Leu	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	166	46	0.277108	NM_176820	B2RN12|Q86W27	Missense_Mutation	SNP	ENST00000332836.2	37	CCDS12934.1	.	.	.	.	.	.	.	.	.	.	C	14.11	2.436550	0.43224	.	.	ENSG00000185792	ENST00000332836;ENST00000333452	T	0.57595	0.39	3.63	-3.39	0.04868	Pyrin (2);DEATH-like (2);	.	.	.	.	T	0.47581	0.1453	L	0.39020	1.185	0.09310	N	1	P	0.46395	0.877	P	0.51016	0.656	T	0.48647	-0.9017	9	0.33141	T	0.24	.	9.9981	0.41911	0.1498:0.2618:0.5884:0.0	.	71	Q7RTR0	NALP9_HUMAN	L	71	ENSP00000331857:V71L	ENSP00000331857:V71L	V	-	1	0	NLRP9	60941342	0.080000	0.21391	0.000000	0.03702	0.011000	0.07611	-0.007000	0.12810	-0.423000	0.07394	-0.175000	0.13238	GTA	.	.	none		0.493	NLRP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453653.1	NM_176820	
MEF2A	4205	hgsc.bcm.edu	37	15	100246936	100246936	+	Silent	SNP	T	T	C	rs325408|rs17854846	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr15:100246936T>C	ENST00000557785.1	+	9	1210	c.861T>C	c.(859-861)aaT>aaC	p.N287N	MEF2A_ENST00000338042.6_Silent_p.N296N|MEF2A_ENST00000557942.1_Silent_p.N295N|MEF2A_ENST00000453228.2_Silent_p.N287N|MEF2A_ENST00000354410.5_Silent_p.N289N|MEF2A_ENST00000449277.2_Silent_p.N219N|MEF2A_ENST00000558812.1_Silent_p.N227N	NM_001171894.1	NP_001165365.1	Q02078	MEF2A_HUMAN	myocyte enhancer factor 2A	297					apoptotic process (GO:0006915)|cardiac conduction (GO:0061337)|cellular response to calcium ion (GO:0071277)|dendrite morphogenesis (GO:0048813)|ERK5 cascade (GO:0070375)|heart development (GO:0007507)|innate immune response (GO:0045087)|MAPK cascade (GO:0000165)|mitochondrial genome maintenance (GO:0000002)|mitochondrion distribution (GO:0048311)|muscle cell differentiation (GO:0042692)|muscle organ development (GO:0007517)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|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)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|ventricular cardiac myofibril assembly (GO:0055005)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	activating transcription factor binding (GO:0033613)|chromatin binding (GO:0003682)|histone acetyltransferase binding (GO:0035035)|histone deacetylase binding (GO:0042826)|protein heterodimerization activity (GO:0046982)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription coactivator activity (GO:0001105)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|SMAD binding (GO:0046332)			endometrium(2)|large_intestine(2)|lung(7)|ovary(1)	12	Lung NSC(78;0.00335)|all_lung(78;0.00659)|Melanoma(26;0.00778)|Medulloblastoma(229;0.163)		OV - Ovarian serous cystadenocarcinoma(32;0.00085)			TCTCACAGAATACCCAGAGGA	0.408													T|||	3067	0.61242	0.2057	0.6369	5008	,	,		16617	0.7103		0.7922	False		,,,				2504	0.8589				p.N289N		Atlas-SNP	.											.	MEF2A	138	.	0			c.T867C						PASS	.	T	,,,,	1234,2640		200,834,903	88.0	78.0	81.0		861,681,657,861,867	-1.8	0.8	15	dbSNP_79	81	6551,1727		2598,1355,186	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	MEF2A	NM_001130926.1,NM_001130927.1,NM_001130928.1,NM_001171894.1,NM_005587.2	,,,,	2798,2189,1089	CC,CT,TT		20.8625,31.8534,35.9365	,,,,	287/498,227/438,219/430,287/498,289/500	100246936	7785,4367	1937	4139	6076	SO:0001819	synonymous_variant	4205	exon9			ACAGAATACCCAG		CCDS45362.1, CCDS45363.1, CCDS53978.1, CCDS58401.1	15q26	2008-02-05	2007-04-24			ENSG00000068305		"""Myocyte enhancer factors"""	6993	protein-coding gene	gene with protein product		600660				1516833	Standard	NM_005587		Approved	RSRFC4, RSRFC9	uc002bvf.3	Q02078		ENST00000557785.1:c.861T>C	15.37:g.100246936T>C		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	94	4	0.0425532	NM_005587	B4DFQ7|F6XG23|O43814|Q14223|Q14224|Q59GX4|Q7Z6C9|Q96D14	Silent	SNP	ENST00000557785.1	37	CCDS53978.1																																																																																			T|0.332;C|0.668	0.668	strong		0.408	MEF2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415985.1		
PRDM9	56979	hgsc.bcm.edu	37	5	23527724	23527724	+	Missense_Mutation	SNP	A	A	G			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr5:23527724A>G	ENST00000296682.3	+	11	2709	c.2527A>G	c.(2527-2529)Aat>Gat	p.N843D		NM_020227.2	NP_064612.2	Q9NQV7	PRDM9_HUMAN	PR domain containing 9	843					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)	p.N843D(2)		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						GGGCTTTCGCAATAAGTCACA	0.587										HNSCC(3;0.000094)																											p.N843D		Atlas-SNP	.											PRDM9,trunk,malignant_melanoma,0,2	PRDM9	344	2	2	Substitution - Missense(2)	skin(2)	c.A2527G						scavenged	.						66.0	76.0	72.0					5																	23527724		2183	4295	6478	SO:0001583	missense	56979	exon11			TTTCGCAATAAGT	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.2527A>G	5.37:g.23527724A>G	ENSP00000296682:p.Asn843Asp	Somatic	237	3	0.0126582		WXS	Illumina HiSeq	Phase_I	195	8	0.0410256	NM_020227	B4DX22|Q27Q50	Missense_Mutation	SNP	ENST00000296682.3	37	CCDS43307.1	.	.	.	.	.	.	.	.	.	.	a	0	-2.847213	0.00067	.	.	ENSG00000164256	ENST00000296682	T	0.07444	3.19	2.67	-5.34	0.02705	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.02848	0.0085	N	0.04355	-0.22	0.09310	N	1	B	0.06786	0.001	B	0.11329	0.006	T	0.30208	-0.9986	9	0.32370	T	0.25	.	1.9842	0.03433	0.2035:0.1472:0.4036:0.2457	.	843	Q9NQV7	PRDM9_HUMAN	D	843	ENSP00000296682:N843D	ENSP00000296682:N843D	N	+	1	0	PRDM9	23563481	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-14.808000	0.00000	-5.282000	0.00017	-3.452000	0.00036	AAT	.	.	none		0.587	PRDM9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366375.1	NM_020227	
ZNF813	126017	hgsc.bcm.edu	37	19	53993764	53993764	+	Missense_Mutation	SNP	A	A	T	rs12609217	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr19:53993764A>T	ENST00000396403.4	+	4	406	c.278A>T	c.(277-279)gAt>gTt	p.D93V	ZNF813_ENST00000396421.4_Intron	NM_001004301.3	NP_001004301.2	Q6ZN06	ZN813_HUMAN	zinc finger protein 813	93			D -> V (in dbSNP:rs12609217).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			large_intestine(1)	1				GBM - Glioblastoma multiforme(134;0.00619)		ATTGATAAAGATATTCATAAC	0.398													a|||	301	0.0601038	0.0	0.0634	5008	,	,		20095	0.2401		0.003	False		,,,				2504	0.0123				p.D93V		Atlas-SNP	.											ZNF813_ENST00000396403,NS,carcinoma,+1,1	ZNF813	81	1	0			c.A278T						scavenged	.	A	VAL/ASP	8,4384	12.9+/-30.5	0,8,2188	91.0	97.0	95.0		278	0.5	0.0	19	dbSNP_120	95	8,8588	7.1+/-27.0	0,8,4290	yes	missense	ZNF813	NM_001004301.3	152	0,16,6478	TT,TA,AA		0.0931,0.1821,0.1232	probably-damaging	93/618	53993764	16,12972	2196	4298	6494	SO:0001583	missense	126017	exon4			ATAAAGATATTCA	AK091460	CCDS46172.1	19q13.41	2013-01-08			ENSG00000198346	ENSG00000198346		"""Zinc fingers, C2H2-type"", ""-"""	33257	protein-coding gene	gene with protein product							Standard	NM_001004301		Approved	FLJ16542	uc002qbu.2	Q6ZN06	OTTHUMG00000158309	ENST00000396403.4:c.278A>T	19.37:g.53993764A>T	ENSP00000379684:p.Asp93Val	Somatic	286	0	0		WXS	Illumina HiSeq	Phase_I	303	6	0.019802	NM_001004301		Missense_Mutation	SNP	ENST00000396403.4	37	CCDS46172.1	149	0.06822344322344322	0	0.0	13	0.03591160220994475	133	0.23251748251748253	3	0.00395778364116095	A	10.25	1.299475	0.23650	0.001821	9.31E-4	ENSG00000198346	ENST00000468450;ENST00000396403;ENST00000490956	T;T;T	0.05786	3.94;3.39;5.03	0.467	0.467	0.16721	.	.	.	.	.	T	0.00012	0.0000	L	0.38838	1.175	0.80722	P	0.0	D	0.63046	0.992	D	0.68039	0.955	T	0.45659	-0.9246	8	0.30078	T	0.28	.	5.1617	0.15064	0.9999:0.0:1.0E-4:0.0	rs12609217;rs52817570;rs12609217	93	Q6ZN06	ZN813_HUMAN	V	40;93;124	ENSP00000419821:D40V;ENSP00000379684:D93V;ENSP00000418289:D124V	ENSP00000379684:D93V	D	+	2	0	ZNF813	58685576	0.052000	0.20516	0.003000	0.11579	0.140000	0.21249	0.867000	0.27968	0.393000	0.25203	0.172000	0.16884	GAT	A|0.945;T|0.055	0.055	strong		0.398	ZNF813-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350638.1	NM_001004301	
MUC6	4588	hgsc.bcm.edu	37	11	1016851	1016851	+	Missense_Mutation	SNP	T	T	C			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr11:1016851T>C	ENST00000421673.2	-	31	6000	c.5950A>G	c.(5950-5952)Atg>Gtg	p.M1984V		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	1984	Thr-rich.				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)		GTTGCAGTCATAGGACCTGTG	0.582																																					p.M1984V		Atlas-SNP	.											MUC6_ENST00000421673,NS,carcinoma,+2,2	MUC6	408	2	0			c.A5950G						scavenged	.						1531.0	1522.0	1525.0					11																	1016851		2203	4298	6501	SO:0001583	missense	4588	exon31			CAGTCATAGGACC	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.5950A>G	11.37:g.1016851T>C	ENSP00000406861:p.Met1984Val	Somatic	677	21	0.0310192		WXS	Illumina HiSeq	Phase_I	754	29	0.0384615	NM_005961	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	Missense_Mutation	SNP	ENST00000421673.2	37	CCDS44513.1	.	.	.	.	.	.	.	.	.	.	C	1.757	-0.487796	0.04352	.	.	ENSG00000184956	ENST00000421673	T	0.17370	2.28	2.75	-1.23	0.09465	.	.	.	.	.	T	0.10809	0.0264	L	0.43152	1.355	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.45205	-0.9277	9	0.06365	T	0.9	.	7.0983	0.25321	0.0:0.1589:0.2688:0.5723	.	1984	Q6W4X9	MUC6_HUMAN	V	1984	ENSP00000406861:M1984V	ENSP00000406861:M1984V	M	-	1	0	MUC6	1006851	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-3.137000	0.00588	-0.732000	0.04856	-2.319000	0.00253	ATG	.	.	none		0.582	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382120.2	XM_290540	
ESRP1	54845	hgsc.bcm.edu	37	8	95680229	95680229	+	Silent	SNP	C	C	T	rs1549466	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr8:95680229C>T	ENST00000433389.2	+	10	1174	c.984C>T	c.(982-984)gtC>gtT	p.V328V	ESRP1_ENST00000423620.2_Silent_p.V328V|ESRP1_ENST00000454170.2_Silent_p.V328V|ESRP1_ENST00000358397.5_Silent_p.V328V	NM_001034915.2|NM_017697.3	NP_001030087.2|NP_060167.2	Q6NXG1	ESRP1_HUMAN	epithelial splicing regulatory protein 1	328	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				mRNA processing (GO:0006397)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)		ESRP1/RAF1(4)	NS(1)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(2)|lung(6)|prostate(1)|urinary_tract(2)	20						AAGTCATTGTCCGCATGCGGG	0.483													C|||	1765	0.352436	0.0514	0.3804	5008	,	,		19140	0.5387		0.3897	False		,,,				2504	0.5092				p.V328V		Atlas-SNP	.											ESRP1_ENST00000433389,NS,carcinoma,+2,2	ESRP1	148	2	0			c.C984T						scavenged	.	C	,,,,	393,3341		21,351,1495	61.0	60.0	60.0		984,984,984,984,984	-0.6	1.0	8	dbSNP_88	60	3101,5085		579,1943,1571	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ESRP1	NM_001034915.2,NM_001122825.1,NM_001122826.1,NM_001122827.1,NM_017697.3	,,,,	600,2294,3066	TT,TC,CC		37.8817,10.5249,29.3121	,,,,	328/678,328/609,328/660,328/605,328/682	95680229	3494,8426	1867	4093	5960	SO:0001819	synonymous_variant	54845	exon10			CATTGTCCGCATG	AK000178	CCDS47895.1, CCDS47896.1, CCDS47897.1, CCDS47898.1	8q22.1	2013-02-12	2009-03-10	2009-03-10	ENSG00000104413	ENSG00000104413		"""RNA binding motif (RRM) containing"""	25966	protein-coding gene	gene with protein product		612959	"""RNA binding motif protein 35A"""	RBM35A		12477932	Standard	NM_017697		Approved	FLJ20171	uc003ygq.4	Q6NXG1	OTTHUMG00000164587	ENST00000433389.2:c.984C>T	8.37:g.95680229C>T		Somatic	120	1	0.00833333		WXS	Illumina HiSeq	Phase_I	138	4	0.0289855	NM_001122827	A6NHA8|A8MPX1|E9PB47|Q2M2B0|Q499G3|Q6PJ86|Q9NXL8	Silent	SNP	ENST00000433389.2	37	CCDS47897.1	780	0.35714285714285715	28	0.056910569105691054	135	0.3729281767955801	307	0.5367132867132867	310	0.40897097625329815	C	9.611	1.131193	0.21041	0.105249	0.378817	ENSG00000104413	ENST00000519505	.	.	.	5.78	-0.637	0.11504	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.47761	-0.9092	3	.	.	.	-9.6706	9.8714	0.41177	0.0:0.28:0.5332:0.1868	rs1549466;rs17717111;rs1549466	.	.	.	S	194	.	.	P	+	1	0	ESRP1	95749405	0.112000	0.22096	0.981000	0.43875	0.994000	0.84299	-0.523000	0.06230	-0.440000	0.07211	-0.302000	0.09304	CCG	C|0.648;T|0.352	0.352	strong		0.483	ESRP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379326.1	NM_017697	
SLC2A8	29988	hgsc.bcm.edu	37	9	130164993	130164993	+	Silent	SNP	C	C	T	rs1138739	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr9:130164993C>T	ENST00000373371.3	+	5	773	c.684C>T	c.(682-684)tcC>tcT	p.S228S	SLC2A8_ENST00000373352.1_Intron|SLC2A8_ENST00000373360.3_Silent_p.S228S	NM_001271712.1|NM_014580.3	NP_001258641.1|NP_055395.2	Q9NY64	GTR8_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 8	228					carbohydrate metabolic process (GO:0005975)|glucose transport (GO:0015758)|insulin receptor signaling pathway (GO:0008286)|male meiosis I (GO:0007141)|response to hypoxia (GO:0001666)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	glucose binding (GO:0005536)|glucose transmembrane transporter activity (GO:0005355)			cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(2)|ovary(1)	11						TGTGGGGCTCCGAGCAGGGCT	0.667													C|||	909	0.18151	0.0287	0.3905	5008	,	,		18586	0.1994		0.2495	False		,,,				2504	0.1513				p.S228S		Atlas-SNP	.											.	SLC2A8	27	.	0			c.C684T						PASS	.	C		247,4079		7,233,1923	13.0	13.0	13.0		684	-6.5	0.5	9	dbSNP_86	13	1703,6815		179,1345,2735	no	coding-synonymous	SLC2A8	NM_014580.3		186,1578,4658	TT,TC,CC		19.993,5.7097,15.1822		228/478	130164993	1950,10894	2163	4259	6422	SO:0001819	synonymous_variant	29988	exon5			GGGCTCCGAGCAG	AJ245937	CCDS6870.1, CCDS65138.1, CCDS75903.1	9q33.3	2013-05-22	2008-09-02		ENSG00000136856	ENSG00000136856		"""Solute carriers"""	13812	protein-coding gene	gene with protein product		605245	"""solute carrier family 2 (facilitated glucose transporter) member 8"""			10671487, 10821868	Standard	NM_014580		Approved	GLUTX1, GLUT8	uc004bqu.4	Q9NY64	OTTHUMG00000020702	ENST00000373371.3:c.684C>T	9.37:g.130164993C>T		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	74	4	0.0540541	NM_014580	Q8WUZ9|Q9NSC4	Silent	SNP	ENST00000373371.3	37	CCDS6870.1	468	0.21428571428571427	18	0.036585365853658534	119	0.3287292817679558	134	0.23426573426573427	197	0.2598944591029024	C	8.232	0.804925	0.16467	0.057097	0.19993	ENSG00000136856	ENST00000419132	.	.	.	4.85	-6.51	0.01878	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999292092	.	.	.	.	.	.	T	0.25433	-1.0132	3	.	.	.	.	9.1661	0.37052	0.1166:0.2684:0.0:0.615	rs1138739;rs3202779;rs3802365;rs17425222	.	.	.	L	138	.	.	P	+	2	0	SLC2A8	129204814	0.000000	0.05858	0.475000	0.27278	0.902000	0.53008	-6.055000	0.00083	-1.115000	0.02973	-0.471000	0.05019	CCG	C|0.827;T|0.173	0.173	strong		0.667	SLC2A8-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054177.1	NM_014580	
CLEC18C	283971	hgsc.bcm.edu	37	16	70211218	70211218	+	Silent	SNP	G	G	A	rs149087931	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr16:70211218G>A	ENST00000569347.2	+	3	545	c.291G>A	c.(289-291)gcG>gcA	p.A97A	CLEC18C_ENST00000536907.2_Silent_p.A97A|CLEC18C_ENST00000561612.1_Intron|CLEC18C_ENST00000541793.2_Silent_p.A97A|CLEC18C_ENST00000314151.8_Silent_p.A97A	NM_173619.2	NP_775890.2	Q8NCF0	CL18C_HUMAN	C-type lectin domain family 18, member C	97	SCP.					extracellular region (GO:0005576)	carbohydrate binding (GO:0030246)			endometrium(3)|large_intestine(6)|lung(1)	10						CGAGCCTGGCGTCCGGCCTGT	0.637																																					p.A97A		Atlas-SNP	.											CLEC18C,NS,carcinoma,0,1	CLEC18C	15	1	0			c.G291A						scavenged	.						4.0	7.0	6.0					16																	70211218		1856	3689	5545	SO:0001819	synonymous_variant	283971	exon3			CCTGGCGTCCGGC	AL833339	CCDS32473.1	16q22.1	2010-04-27	2009-03-10	2009-03-10		ENSG00000157335		"""C-type lectin domain containing"""	28538	protein-coding gene	gene with protein product						12477932	Standard	XM_005255906		Approved	MGC34761		Q8NCF0		ENST00000569347.2:c.291G>A	16.37:g.70211218G>A		Somatic	412	2	0.00485437		WXS	Illumina HiSeq	Phase_I	426	10	0.0234742	NM_173619	Q8IUW8	Silent	SNP	ENST00000569347.2	37	CCDS32473.1	.	.	.	.	.	.	.	.	.	.	N	4.212	0.038195	0.08148	.	.	ENSG00000157335	ENST00000539438	.	.	.	3.67	-7.35	0.01422	.	.	.	.	.	T	0.29684	0.0741	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.31943	-0.9925	5	0.34782	T	0.22	.	7.4304	0.27124	0.5189:0.3372:0.1439:0.0	.	.	.	.	I	95	.	ENSP00000445424:V95I	V	+	1	0	CLEC18C	68768719	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-3.589000	0.00422	-2.515000	0.00501	-0.701000	0.03672	GTC	G|0.925;A|0.075	0.075	strong		0.637	CLEC18C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000434588.2	NM_173619	
LIFR	3977	hgsc.bcm.edu	37	5	38496637	38496637	+	Missense_Mutation	SNP	C	C	T	rs3729740	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr5:38496637C>T	ENST00000263409.4	-	13	1894	c.1732G>A	c.(1732-1734)Gat>Aat	p.D578N	LIFR_ENST00000453190.2_Missense_Mutation_p.D578N|LIFR_ENST00000503088.1_5'UTR	NM_002310.5	NP_002301.1	P42702	LIFR_HUMAN	leukemia inhibitory factor receptor alpha	578	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.		D -> N (in dbSNP:rs3729740).		cell surface receptor signaling pathway (GO:0007166)|ciliary neurotrophic factor-mediated signaling pathway (GO:0070120)|cytokine-mediated signaling pathway (GO:0019221)|leukemia inhibitory factor signaling pathway (GO:0048861)|oncostatin-M-mediated signaling pathway (GO:0038165)|positive regulation of cell proliferation (GO:0008284)|response to cytokine (GO:0034097)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	ciliary neurotrophic factor receptor binding (GO:0005127)|growth factor binding (GO:0019838)|leukemia inhibitory factor receptor activity (GO:0004923)	p.D578H(1)		NS(2)|breast(4)|endometrium(6)|kidney(2)|large_intestine(30)|liver(2)|lung(21)|ovary(3)|skin(5)|stomach(1)|urinary_tract(2)	78	all_lung(31;0.00021)					GTTTCCTCATCTGATGAACAC	0.373			T	PLAG1	salivary adenoma								C|||	263	0.052516	0.0008	0.0144	5008	,	,		24131	0.2411		0.002	False		,,,				2504	0.0072				p.D578N	Melanoma(13;4 730 6426 9861 34751)	Atlas-SNP	.		Dom	yes		5	5p13-p12	3977	leukemia inhibitory factor receptor		E	LIFR,NS,NS,0,1	LIFR	348	1	1	Substitution - Missense(1)	NS(1)	c.G1732A						PASS	.	C	ASN/ASP,ASN/ASP	6,4400	11.4+/-27.6	0,6,2197	208.0	177.0	187.0		1732,1732	1.9	0.0	5	dbSNP_107	187	12,8588	9.1+/-34.3	0,12,4288	yes	missense,missense	LIFR	NM_001127671.1,NM_002310.5	23,23	0,18,6485	TT,TC,CC		0.1395,0.1362,0.1384	benign,benign	578/1098,578/1098	38496637	18,12988	2203	4300	6503	SO:0001583	missense	3977	exon13			CCTCATCTGATGA	X61615	CCDS3927.1	5p13-p12	2013-02-11	2006-05-17		ENSG00000113594	ENSG00000113594		"""CD molecules"", ""Fibronectin type III domain containing"""	6597	protein-coding gene	gene with protein product		151443	"""leukemia inhibitory factor receptor"""			1915266	Standard	NM_001127671		Approved	CD118	uc003jli.2	P42702	OTTHUMG00000131138	ENST00000263409.4:c.1732G>A	5.37:g.38496637C>T	ENSP00000263409:p.Asp578Asn	Somatic	179	0	0		WXS	Illumina HiSeq	Phase_I	152	7	0.0460526	NM_002310	Q6LCD9	Missense_Mutation	SNP	ENST00000263409.4	37	CCDS3927.1	137	0.06272893772893773	0	0.0	3	0.008287292817679558	134	0.23426573426573427	0	0.0	C	12.10	1.836874	0.32421	0.001362	0.001395	ENSG00000113594	ENST00000263409;ENST00000453190	T;T	0.53423	0.62;0.62	5.73	1.88	0.25563	Fibronectin, type III (3);Immunoglobulin-like fold (1);	1.341120	0.04080	N	0.309436	T	0.00012	0.0000	N	0.02539	-0.55	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.15378	-1.0439	9	0.18710	T	0.47	-6.449	4.778	0.13189	0.0:0.3771:0.311:0.3119	rs3729740;rs52801382;rs56643611;rs3729740	578	P42702	LIFR_HUMAN	N	578	ENSP00000263409:D578N;ENSP00000398368:D578N	ENSP00000263409:D578N	D	-	1	0	LIFR	38532394	0.000000	0.05858	0.001000	0.08648	0.907000	0.53573	0.429000	0.21412	0.323000	0.23307	0.563000	0.77884	GAT	C|0.969;T|0.031	0.031	strong		0.373	LIFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253823.1	NM_002310	
SATB2	23314	hgsc.bcm.edu	37	2	200173610	200173610	+	Missense_Mutation	SNP	A	A	G			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr2:200173610A>G	ENST00000417098.1	-	10	2429	c.1613T>C	c.(1612-1614)cTc>cCc	p.L538P	SATB2_ENST00000457245.1_Missense_Mutation_p.L538P|SATB2_ENST00000428695.1_Missense_Mutation_p.L420P|SATB2_ENST00000260926.5_Missense_Mutation_p.L538P|SATB2_ENST00000443023.1_Missense_Mutation_p.L479P	NM_001172509.1	NP_001165980.1	Q9UPW6	SATB2_HUMAN	SATB homeobox 2	538					cartilage development (GO:0051216)|cellular response to organic substance (GO:0071310)|chromatin remodeling (GO:0006338)|embryonic pattern specification (GO:0009880)|embryonic skeletal system morphogenesis (GO:0048704)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron migration (GO:0001764)|osteoblast development (GO:0002076)|palate development (GO:0060021)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|histone deacetylase complex (GO:0000118)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|sequence-specific DNA binding (GO:0043565)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(40)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	62						GATGGTACAGAGGTTTTCCCA	0.557																																					p.L538P	Colon(30;262 767 11040 24421 36230)	Atlas-SNP	.											.	SATB2	134	.	0			c.T1613C						PASS	.						132.0	106.0	115.0					2																	200173610		2203	4300	6503	SO:0001583	missense	23314	exon11			GTACAGAGGTTTT	AB028957	CCDS2327.1	2q33.1	2011-06-20	2007-02-15		ENSG00000119042	ENSG00000119042		"""Homeoboxes / CUT class"""	21637	protein-coding gene	gene with protein product		608148	"""SATB family member 2"""				Standard	NM_015265		Approved	KIAA1034, FLJ21474	uc002uva.2	Q9UPW6	OTTHUMG00000132767	ENST00000417098.1:c.1613T>C	2.37:g.200173610A>G	ENSP00000401112:p.Leu538Pro	Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	119	47	0.394958	NM_015265	A8K5Z8|Q3ZB87|Q4V763	Missense_Mutation	SNP	ENST00000417098.1	37	CCDS2327.1	.	.	.	.	.	.	.	.	.	.	A	27.5	4.838366	0.91117	.	.	ENSG00000119042	ENST00000417098;ENST00000443023;ENST00000260926;ENST00000428695;ENST00000457245	T;T;T;T;T	0.61980	0.18;0.19;0.18;0.06;0.18	5.21	5.21	0.72293	Homeodomain protein CUT (2);Lambda repressor-like, DNA-binding (2);	0.000000	0.85682	D	0.000000	T	0.78188	0.4244	M	0.70275	2.135	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.97110	0.999;1.0	T	0.80879	-0.1185	10	0.87932	D	0	-15.8414	15.5441	0.76081	1.0:0.0:0.0:0.0	.	420;538	Q3ZB87;Q9UPW6	.;SATB2_HUMAN	P	538;479;538;420;538	ENSP00000401112:L538P;ENSP00000388764:L479P;ENSP00000260926:L538P;ENSP00000388581:L420P;ENSP00000405420:L538P	ENSP00000260926:L538P	L	-	2	0	SATB2	199881855	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.087000	0.94110	2.317000	0.78254	0.459000	0.35465	CTC	.	.	none		0.557	SATB2-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256140.1	NM_015265	
NOTCH4	4855	hgsc.bcm.edu	37	6	32188823	32188823	+	Missense_Mutation	SNP	G	G	A	rs8192585	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr6:32188823G>A	ENST00000375023.3	-	4	869	c.731C>T	c.(730-732)tCg>tTg	p.S244L		NM_004557.3	NP_004548.3	Q99466	NOTC4_HUMAN	notch 4	244	EGF-like 6. {ECO:0000255|PROSITE- ProRule:PRU00076}.		S -> L (in dbSNP:rs8192585).		cell differentiation (GO:0030154)|cell fate determination (GO:0001709)|embryo development (GO:0009790)|endothelial cell morphogenesis (GO:0001886)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|mammary gland development (GO:0030879)|morphogenesis of a branching structure (GO:0001763)|negative regulation of cell differentiation (GO:0045596)|negative regulation of endothelial cell differentiation (GO:0045602)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|patterning of blood vessels (GO:0001569)|positive regulation of transcription of Notch receptor target (GO:0007221)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cell surface (GO:0009986)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|protein heterodimerization activity (GO:0046982)|receptor activity (GO:0004872)			NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(4)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(47)|ovary(5)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(1)	100						GCCCCCATTCGAACAGCCCCT	0.657													G|||	111	0.0221645	0.0151	0.0173	5008	,	,		19615	0.0149		0.0378	False		,,,				2504	0.0266				p.S244L		Atlas-SNP	.											.	NOTCH4	201	.	0			c.C731T						PASS	.	G	LEU/SER	52,2970		0,52,1459	71.0	60.0	64.0		731	-6.9	0.0	6	dbSNP_117	64	207,5211		4,199,2506	yes	missense	NOTCH4	NM_004557.3	145	4,251,3965	AA,AG,GG		3.8206,1.7207,3.0687	benign	244/2004	32188823	259,8181	1511	2709	4220	SO:0001583	missense	4855	exon4			CCATTCGAACAGC		CCDS34420.1	6p21.3	2013-01-10	2010-06-24		ENSG00000204301	ENSG00000204301		"""Ankyrin repeat domain containing"""	7884	protein-coding gene	gene with protein product		164951	"""Notch (Drosophila) homolog 4"", ""Notch homolog 4 (Drosophila)"""	INT3		7835890	Standard	NM_004557		Approved		uc003obb.3	Q99466	OTTHUMG00000031044	ENST00000375023.3:c.731C>T	6.37:g.32188823G>A	ENSP00000364163:p.Ser244Leu	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	51	4	0.0784314	NM_004557	B0V183|B0V1X5|O00306|Q5SSY7|Q99458|Q99940|Q9H3S8|Q9UII9|Q9UIJ0	Missense_Mutation	SNP	ENST00000375023.3	37	CCDS34420.1	63	0.028846153846153848	13	0.026422764227642278	6	0.016574585635359115	12	0.02097902097902098	32	0.04221635883905013	G	0.030	-1.341388	0.01277	0.017207	0.038206	ENSG00000204301	ENST00000375023	D	0.92647	-3.08	4.74	-6.92	0.01644	EGF (1);Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	0.952505	0.08556	N	0.928307	T	0.48696	0.1514	N	0.00648	-1.295	0.54753	D	0.999987	B;B	0.09022	0.001;0.002	B;B	0.09377	0.004;0.002	T	0.04140	-1.0974	10	0.07175	T	0.84	.	10.6497	0.45640	0.7392:0.0:0.1481:0.1127	rs8192585;rs61279185;rs8192585	244;244	Q6P3V5;Q99466	.;NOTC4_HUMAN	L	244	ENSP00000364163:S244L	ENSP00000364163:S244L	S	-	2	0	NOTCH4	32296801	0.000000	0.05858	0.009000	0.14445	0.146000	0.21551	-1.565000	0.02150	-1.259000	0.02468	-0.424000	0.05967	TCG	G|0.969;A|0.031	0.031	strong		0.657	NOTCH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076045.2		
DNASE2B	58511	hgsc.bcm.edu	37	1	84864256	84864256	+	Missense_Mutation	SNP	G	G	C	rs3738573	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr1:84864256G>C	ENST00000370665.3	+	1	42	c.9G>C	c.(7-9)caG>caC	p.Q3H		NM_021233.2	NP_067056.2	Q8WZ79	DNS2B_HUMAN	deoxyribonuclease II beta	3			Q -> H (in dbSNP:rs3738573).		apoptotic DNA fragmentation (GO:0006309)	extracellular region (GO:0005576)|intracellular (GO:0005622)|lysosome (GO:0005764)	deoxyribonuclease II activity (GO:0004531)			endometrium(1)|lung(4)|skin(1)	6				all cancers(265;0.00303)|Epithelial(280;0.0112)|OV - Ovarian serous cystadenocarcinoma(397;0.0808)		AAATGAAACAGAAAATGATGG	0.468													G|||	1473	0.294129	0.1755	0.3156	5008	,	,		20991	0.4038		0.334	False		,,,				2504	0.2853				p.Q3H	Pancreas(54;788 1175 11852 16034 30034)	Atlas-SNP	.											DNASE2B_ENST00000370665,NS,carcinoma,0,1	DNASE2B	40	1	0			c.G9C						scavenged	.	G	HIS/GLN	778,3356		79,620,1368	166.0	174.0	171.0		9	3.0	0.8	1	dbSNP_107	171	2894,5546		499,1896,1825	yes	missense	DNASE2B	NM_021233.2	24	578,2516,3193	CC,CG,GG		34.2891,18.8195,29.2031	benign	3/362	84864256	3672,8902	2067	4220	6287	SO:0001583	missense	58511	exon1			GAAACAGAAAATG	AF274571	CCDS694.1, CCDS44167.1	1p22.3	2008-02-05			ENSG00000137976	ENSG00000137976			28875	protein-coding gene	gene with protein product		608057				12594037, 11376952	Standard	NM_021233		Approved	DLAD	uc001djt.1	Q8WZ79	OTTHUMG00000009860	ENST00000370665.3:c.9G>C	1.37:g.84864256G>C	ENSP00000359699:p.Gln3His	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	76	3	0.0394737	NM_021233	Q5VXD0|Q5VXD1|Q8WZ80|Q9NQW3	Missense_Mutation	SNP	ENST00000370665.3	37	CCDS44167.1	658	0.30128205128205127	94	0.1910569105691057	107	0.2955801104972376	211	0.3688811188811189	246	0.3245382585751979	G	0.349	-0.945820	0.02304	0.188195	0.342891	ENSG00000137976	ENST00000370665	T	0.11821	2.74	4.91	2.99	0.34606	.	0.945862	0.08788	N	0.893617	T	0.02083	0.0065	N	0.08118	0	0.09310	P	0.9999999400257	P	0.37864	0.61	B	0.35550	0.205	T	0.44421	-0.9329	9	0.26408	T	0.33	2.9062	7.0606	0.25123	0.2131:0.0:0.7869:0.0	rs3738573;rs17479406;rs3738573	3	Q8WZ79	DNS2B_HUMAN	H	3	ENSP00000359699:Q3H	ENSP00000359699:Q3H	Q	+	3	2	DNASE2B	84636844	0.616000	0.27035	0.798000	0.32154	0.152000	0.21847	0.646000	0.24797	0.742000	0.32697	0.655000	0.94253	CAG	G|0.694;C|0.306	0.306	strong		0.468	DNASE2B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000027248.1	NM_021233	
MTHFD1L	25902	hgsc.bcm.edu	37	6	151336739	151336739	+	Silent	SNP	C	C	G	rs509474	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr6:151336739C>G	ENST00000367321.3	+	24	2770	c.2496C>G	c.(2494-2496)tcC>tcG	p.S832S		NM_001242767.1|NM_001242768.1|NM_015440.4	NP_001229696.1|NP_001229697.1|NP_056255.2	Q6UB35	C1TM_HUMAN	methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1-like	832	Formyltetrahydrofolate synthetase.				folic acid-containing compound biosynthetic process (GO:0009396)|folic acid-containing compound metabolic process (GO:0006760)|formate metabolic process (GO:0015942)|one-carbon metabolic process (GO:0006730)|oxidation-reduction process (GO:0055114)|tetrahydrofolate interconversion (GO:0035999)|tetrahydrofolate metabolic process (GO:0046653)	membrane (GO:0016020)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|formate-tetrahydrofolate ligase activity (GO:0004329)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(12)|lung(8)|ovary(3)|prostate(1)|upper_aerodigestive_tract(2)	29		Ovarian(120;0.128)		OV - Ovarian serous cystadenocarcinoma(155;8.7e-12)		ATCACTGGTCCGTTGGTGGAA	0.527													G|||	2856	0.570288	0.8585	0.4726	5008	,	,		17253	0.6766		0.4374	False		,,,				2504	0.2771				p.S833S		Atlas-SNP	.											.	MTHFD1L	75	.	0			c.C2499G						PASS	.	G	,,	3504,902	349.3+/-310.3	1396,712,95	141.0	126.0	131.0		2499,2301,2496	-7.9	0.0	6	dbSNP_83	131	3846,4754	610.3+/-395.7	862,2122,1316	no	coding-synonymous,coding-synonymous,coding-synonymous	MTHFD1L	NM_001242767.1,NM_001242768.1,NM_015440.4	,,	2258,2834,1411	GG,GC,CC		44.7209,20.4721,43.4876	,,	833/980,767/914,832/979	151336739	7350,5656	2203	4300	6503	SO:0001819	synonymous_variant	25902	exon24			CTGGTCCGTTGGT	BC017477	CCDS5228.1, CCDS56457.1, CCDS75535.1, CCDS75536.1	6q25.1	2010-07-19	2004-12-13	2004-12-14	ENSG00000120254	ENSG00000120254	6.3.4.3		21055	protein-coding gene	gene with protein product	"""10-formyl-THF synthetase"", ""mitochondrial C1-tetrahydrofolate synthase"", ""monofunctional C1-tetrahydrofolate synthase, mitochondrial"""	611427	"""formyltetrahydrofolate synthetase domain containing 1"""	FTHFSDC1		18804703	Standard	NM_015440		Approved	DKFZP586G1517, FLJ21145	uc021zgs.1	Q6UB35	OTTHUMG00000015828	ENST00000367321.3:c.2496C>G	6.37:g.151336739C>G		Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	172	7	0.0406977	NM_001242767	Q2TBF3|Q8WVW0|Q96HG8|Q9H789|Q9UFU8	Silent	SNP	ENST00000367321.3	37	CCDS5228.1																																																																																			C|0.428;G|0.572	0.572	strong		0.527	MTHFD1L-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042699.1	NM_015440	
HTT	3064	hgsc.bcm.edu	37	4	3162056	3162056	+	Silent	SNP	C	C	T	rs363099	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr4:3162056C>T	ENST00000355072.5	+	29	3946	c.3801C>T	c.(3799-3801)ctC>ctT	p.L1267L		NM_002111.6	NP_002102	P42858	HD_HUMAN	huntingtin	1267					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)		GAGGGTTTCTCCGCTCAGCCT	0.507													C|||	1071	0.213858	0.0113	0.2882	5008	,	,		19711	0.3442		0.3121	False		,,,				2504	0.1994				p.L1267L		Atlas-SNP	.											HTT,NS,carcinoma,0,1	HTT	221	1	0			c.C3801T						PASS	.	C		256,3662		16,224,1719	171.0	165.0	167.0		3801	0.1	1.0	4	dbSNP_79	167	2331,5887		331,1669,2109	no	coding-synonymous	HTT	NM_002111.6		347,1893,3828	TT,TC,CC		28.3646,6.5339,21.3167		1267/3143	3162056	2587,9549	1959	4109	6068	SO:0001819	synonymous_variant	3064	exon29			GTTTCTCCGCTCA	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.3801C>T	4.37:g.3162056C>T		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	144	6	0.0416667	NM_002111	Q9UQB7	Silent	SNP	ENST00000355072.5	37	CCDS43206.1																																																																																			T|0.148;G|0.337	0.148	strong		0.507	HTT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358234.2	NM_002111	
PSG11	5680	hgsc.bcm.edu	37	19	43519362	43519362	+	Silent	SNP	C	C	T	rs11083680	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr19:43519362C>T	ENST00000401740.1	-	4	973	c.870G>A	c.(868-870)caG>caA	p.Q290Q	PSG11_ENST00000403486.1_Silent_p.Q168Q|PSG11_ENST00000320078.7_Silent_p.Q290Q|PSG11_ENST00000595312.1_5'Flank|PSG11_ENST00000306322.7_Silent_p.Q168Q			Q00887	PSG9_HUMAN	pregnancy specific beta-1-glycoprotein 11	299	Ig-like C2-type 2.				female pregnancy (GO:0007565)	extracellular region (GO:0005576)				breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(15)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	26		Prostate(69;0.00682)				TTGGAGTAATCTGAGGGATAA	0.458													.|||	3243	0.647564	0.6551	0.4986	5008	,	,		20620	0.9871		0.4751	False		,,,				2504	0.5706				p.Q290Q		Atlas-SNP	.											PSG11,right_lower_lobe,carcinoma,-2,1	PSG11	57	1	0			c.G870A						PASS	.	T	,,	2884,1514	479.9+/-358.7	986,912,301	163.0	162.0	162.0		504,870,504	-0.8	0.0	19	dbSNP_120	162	3875,4719	606.8+/-395.2	915,2045,1337	no	coding-synonymous,coding-synonymous,coding-synonymous	PSG11	NM_001113410.1,NM_002785.2,NM_203287.1	,,	1901,2957,1638	TT,TC,CC		45.0896,34.4247,47.9757	,,	168/214,290/336,168/214	43519362	6759,6233	2199	4297	6496	SO:0001819	synonymous_variant	5680	exon4			AGTAATCTGAGGG	U25988	CCDS12614.2, CCDS12615.2	19q13.2	2013-01-29			ENSG00000243130	ENSG00000243130		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9516	protein-coding gene	gene with protein product	"""pregnancy specific beta-1-glycoprotein 13"""	176401		PSG13, PSG14		7794280	Standard	NM_001113410		Approved	MGC22484	uc002ovm.1	Q9UQ72	OTTHUMG00000151546	ENST00000401740.1:c.870G>A	19.37:g.43519362C>T		Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	191	11	0.0575916	NM_002785	B2R869|Q15227|Q15236|Q15237|Q8WW78|Q9UQ73	Silent	SNP	ENST00000401740.1	37	CCDS12614.2																																																																																			C|0.424;T|0.576	0.576	strong		0.458	PSG11-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323079.1	NM_002785	
CCDC102B	79839	hgsc.bcm.edu	37	18	66513615	66513615	+	Missense_Mutation	SNP	A	A	G	rs2187094	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr18:66513615A>G	ENST00000360242.5	+	4	1010	c.893A>G	c.(892-894)aAg>aGg	p.K298R	CCDC102B_ENST00000577772.1_3'UTR|CCDC102B_ENST00000319445.6_Missense_Mutation_p.K298R|CCDC102B_ENST00000584156.1_Missense_Mutation_p.K298R|CCDC102B_ENST00000358653.5_Splice_Site_p.E312E	NM_024781.2	NP_079057	Q68D86	C102B_HUMAN	coiled-coil domain containing 102B	298			K -> R (in dbSNP:rs2187094). {ECO:0000269|PubMed:17974005}.					p.K298R(1)		breast(2)|endometrium(3)|large_intestine(5)|lung(19)|ovary(1)|skin(5)|stomach(1)	36		Esophageal squamous(42;0.0559)|Colorectal(73;0.0604)				TGGAAGTGGAAGTATGAAGAA	0.358													A|||	1842	0.367812	0.0703	0.4467	5008	,	,		12915	0.6438		0.4006	False		,,,				2504	0.3957				p.K298R		Atlas-SNP	.											CCDC102B,NS,carcinoma,0,2	CCDC102B	92	2	1	Substitution - Missense(1)	stomach(1)	c.A893G						scavenged	.	A	ARG/LYS,ARG/LYS	561,3845	245.3+/-254.3	37,487,1679	70.0	70.0	70.0		893,893	4.4	1.0	18	dbSNP_96	70	3289,5311	486.0+/-371.8	639,2011,1650	yes	missense,missense	CCDC102B	NM_001093729.1,NM_024781.2	26,26	676,2498,3329	GG,GA,AA		38.2442,12.7326,29.6017	benign,benign	298/514,298/514	66513615	3850,9156	2203	4300	6503	SO:0001583	missense	79839	exon6			AGTGGAAGTATGA	AK027247	CCDS11996.2	18q22.1	2007-11-14	2006-04-10	2006-04-10	ENSG00000150636	ENSG00000150636			26295	protein-coding gene	gene with protein product			"""chromosome 18 open reading frame 14"", ""aminoacylase 1-like"""	C18orf14, ACY1L		14702039	Standard	NM_001093729		Approved	FLJ23594, HsT1731, AN	uc002lkk.2	Q68D86	OTTHUMG00000132808	ENST00000360242.5:c.893A>G	18.37:g.66513615A>G	ENSP00000353377:p.Lys298Arg	Somatic	431	1	0.00232019		WXS	Illumina HiSeq	Phase_I	307	10	0.0325733	NM_001093729	Q7Z467|Q8NDK7|Q9H5C1	Missense_Mutation	SNP	ENST00000360242.5	37	CCDS11996.2	850	0.3891941391941392	37	0.07520325203252033	156	0.430939226519337	359	0.6276223776223776	298	0.39313984168865435	A	8.901	0.956416	0.18507	0.127326	0.382442	ENSG00000150636	ENST00000319445;ENST00000360242	T;T	0.15256	2.44;2.44	5.56	4.4	0.53042	.	0.000000	0.64402	D	0.000011	T	0.00012	0.0000	L	0.37697	1.125	0.09310	P	1.0	P	0.47034	0.889	B	0.42827	0.399	T	0.11155	-1.0599	9	0.18710	T	0.47	-26.3717	9.5041	0.39035	0.9196:0.0:0.0804:0.0	rs2187094;rs52829798;rs58141486;rs2187094	298	Q68D86	C102B_HUMAN	R	298	ENSP00000316237:K298R;ENSP00000353377:K298R	ENSP00000316237:K298R	K	+	2	0	CCDC102B	64664595	1.000000	0.71417	0.998000	0.56505	0.313000	0.28021	2.635000	0.46537	1.043000	0.40175	0.528000	0.53228	AAG	A|0.674;G|0.326	0.326	strong		0.358	CCDC102B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256225.2	NM_024781	
CBX3	11335	hgsc.bcm.edu	37	7	26245986	26245986	+	Splice_Site	SNP	A	A	T			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr7:26245986A>T	ENST00000337620.4	+	3	452		c.e3-1		CBX3_ENST00000497498.1_Splice_Site|CBX3_ENST00000396386.2_Splice_Site|CBX3_ENST00000409747.1_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		Somatic	76	1	0.0131579		WXS	Illumina HiSeq	Phase_I	89	6	0.0674157	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
DPH3	285381	hgsc.bcm.edu	37	3	16305674	16305674	+	Silent	SNP	C	C	G	rs14080	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr3:16305674C>G	ENST00000488423.1	-	2	266	c.171G>C	c.(169-171)gtG>gtC	p.V57V	OXNAD1_ENST00000606098.1_5'Flank|OXNAD1_ENST00000435829.2_5'Flank|OXNAD1_ENST00000605932.1_5'Flank|OXNAD1_ENST00000285083.5_5'Flank|DPH3_ENST00000383775.4_Intron|DPH3_ENST00000285082.4_5'UTR	NM_206831.2	NP_996662.1	Q96FX2	DPH3_HUMAN	diphthamide biosynthesis 3	57					negative regulation of protein secretion (GO:0050709)|peptidyl-diphthamide biosynthetic process from peptidyl-histidine (GO:0017183)|positive regulation of binding (GO:0051099)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)			large_intestine(2)	2						TGTCATAAATCACTTTTATAA	0.418													C|||	2172	0.433706	0.3079	0.4712	5008	,	,		17298	0.4762		0.4324	False		,,,				2504	0.5348				p.V57V		Atlas-SNP	.											DPH3,NS,adenoma,0,1	DPH3	7	1	0			c.G171C						scavenged	.	C	,	1546,2860	483.5+/-359.7	274,998,931	107.0	99.0	102.0		,171	3.8	1.0	3	dbSNP_52	102	3648,4952	520.9+/-379.8	782,2084,1434	no	intron,coding-synonymous	DPH3	NM_001047434.2,NM_206831.2	,	1056,3082,2365	GG,GC,CC		42.4186,35.0885,39.9354	,	,57/83	16305674	5194,7812	2203	4300	6503	SO:0001819	synonymous_variant	285381	exon2			ATAAATCACTTTT	BC010181	CCDS2629.1, CCDS43058.1	3p25.1	2013-06-19	2013-06-19	2006-10-25	ENSG00000154813	ENSG00000154813			27717	protein-coding gene	gene with protein product	"""DPH3A, KTI11 homolog A (S. cerevisiae)"""	608959	"""zinc finger, CSL-type containing 2"", ""DPH3 homolog (KTI11, S. cerevisiae)"", ""DPH3, KTI11 homolog (S. cerevisiae)"""	ZCSL2		14527407, 14980502, 15485916, 16648478	Standard	NM_001047434		Approved	DESR1, DELGIP1, MGC20197, KTI11, DELGIP, DPH3A	uc003cau.3	Q96FX2	OTTHUMG00000129866	ENST00000488423.1:c.171G>C	3.37:g.16305674C>G		Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	171	5	0.0292398	NM_206831		Silent	SNP	ENST00000488423.1	37	CCDS2629.1																																																																																			C|0.590;G|0.410	0.410	strong		0.418	DPH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252108.2	NM_206831	
PAK2	5062	hgsc.bcm.edu	37	3	196509522	196509522	+	Missense_Mutation	SNP	C	C	G	rs67093638		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr3:196509522C>G	ENST00000327134.3	+	2	327	c.5C>G	c.(4-6)tCt>tGt	p.S2C	RNU6-42P_ENST00000384165.1_RNA	NM_002577.4	NP_002568.2	Q13177	PAK2_HUMAN	p21 protein (Cdc42/Rac)-activated kinase 2	2					apoptotic process (GO:0006915)|axon guidance (GO:0007411)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis (GO:2001271)|negative regulation of protein kinase activity (GO:0006469)|peptidyl-serine phosphorylation (GO:0018105)|phosphorylation (GO:0016310)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein tyrosine kinase activity (GO:0061098)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of apoptotic process (GO:0042981)|regulation of defense response to virus by virus (GO:0050690)|regulation of growth (GO:0040008)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activator activity (GO:0030296)	p.S2C(2)		breast(1)|cervix(1)|kidney(2)|large_intestine(1)|lung(4)|ovary(1)|prostate(2)	12	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)|Breast(254;0.135)		Epithelial(36;1.07e-23)|all cancers(36;6.38e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.5e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00405)		TGAATCATGTCTGATAACGGA	0.408																																					p.S2C		Atlas-SNP	.											PAK2_ENST00000327134,NS,carcinoma,0,4	PAK2	113	4	2	Substitution - Missense(2)	prostate(2)	c.C5G						scavenged	.						81.0	87.0	85.0					3																	196509522		2203	4300	6503	SO:0001583	missense	5062	exon2			TCATGTCTGATAA	U24153	CCDS3321.1	3q29	2008-06-17	2008-06-17			ENSG00000180370	2.7.11.1		8591	protein-coding gene	gene with protein product	"""S6/H4 kinase"""	605022	"""p21 (CDKN1A)-activated kinase 2"""			7744004, 7618083	Standard	NM_002577		Approved	PAK65, PAKgamma	uc003fwy.4	Q13177		ENST00000327134.3:c.5C>G	3.37:g.196509522C>G	ENSP00000314067:p.Ser2Cys	Somatic	236	2	0.00847458		WXS	Illumina HiSeq	Phase_I	234	5	0.0213675	NM_002577	Q13154|Q6ISC3	Missense_Mutation	SNP	ENST00000327134.3	37	CCDS3321.1	42	0.019230769230769232	6	0.012195121951219513	0	0.0	7	0.012237762237762238	29	0.03825857519788918	C	14.90	2.672409	0.47781	.	.	ENSG00000180370	ENST00000327134	T	0.70631	-0.5	5.21	5.21	0.72293	.	0.055816	0.64402	D	0.000001	T	0.30417	0.0764	N	0.25426	0.745	0.54753	D	0.999985	B	0.15141	0.012	B	0.20577	0.03	T	0.51284	-0.8725	10	0.62326	D	0.03	.	18.756	0.91833	0.0:1.0:0.0:0.0	.	2	Q13177	PAK2_HUMAN	C	2	ENSP00000314067:S2C	ENSP00000314067:S2C	S	+	2	0	PAK2	197993919	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	2.961000	0.49168	2.456000	0.83038	0.655000	0.94253	TCT	C|0.986;G|0.014	0.014	strong		0.408	PAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340548.1	NM_002577	
ZBTB22	9278	hgsc.bcm.edu	37	6	33283766	33283766	+	Missense_Mutation	SNP	T	T	C	rs3130100	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr6:33283766T>C	ENST00000431845.2	-	2	1079	c.928A>G	c.(928-930)Aca>Gca	p.T310A	TAPBP_ENST00000456592.2_5'Flank|TAPBP_ENST00000426633.2_5'Flank|TAPBP_ENST00000489157.1_5'Flank|TAPBP_ENST00000475304.1_5'Flank|ZBTB22_ENST00000418724.1_Missense_Mutation_p.T310A|TAPBP_ENST00000434618.2_5'Flank	NM_005453.4	NP_005444.4	O15209	ZBT22_HUMAN	zinc finger and BTB domain containing 22	310			T -> A (in dbSNP:rs3130100). {ECO:0000269|PubMed:14574404, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		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)|large_intestine(1)|lung(9)|ovary(2)|prostate(1)|urinary_tract(3)	21						ACCAGGGGTGTTGGCGCTGGG	0.567													C|||	2676	0.534345	0.5734	0.549	5008	,	,		18569	0.3899		0.5288	False		,,,				2504	0.6258				p.T310A		Atlas-SNP	.											.	ZBTB22	48	.	0			c.A928G						PASS	.	C	ALA/THR,ALA/THR	2459,1947	544.3+/-376.5	691,1077,435	110.0	91.0	98.0		928,928	3.0	0.6	6	dbSNP_103	98	4652,3948	536.7+/-383.1	1265,2122,913	yes	missense,missense	ZBTB22	NM_001145338.1,NM_005453.4	58,58	1956,3199,1348	CC,CT,TT		45.907,44.1897,45.3252	benign,benign	310/635,310/635	33283766	7111,5895	2203	4300	6503	SO:0001583	missense	9278	exon2			GGGGTGTTGGCGC	Z97183	CCDS4775.1	6p21.3	2013-01-09	2006-04-12	2006-04-12	ENSG00000236104	ENSG00000236104		"""-"", ""BTB/POZ domain containing"", ""Zinc fingers, C2H2-type"""	13085	protein-coding gene	gene with protein product		611439	"""zinc finger protein 297"""	ZNF297			Standard	NM_005453		Approved	BING1, ZNF297A, fruitless, fru, ZBTB22A	uc010juu.3	O15209	OTTHUMG00000031110	ENST00000431845.2:c.928A>G	6.37:g.33283766T>C	ENSP00000407545:p.Thr310Ala	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	92	5	0.0543478	NM_001145338	B0V007|Q5HYV4|Q5STL0|Q5STR7|Q8WV82	Missense_Mutation	SNP	ENST00000431845.2	37	CCDS4775.1	1141	0.5224358974358975	305	0.6199186991869918	218	0.6022099447513812	222	0.3881118881118881	396	0.5224274406332454	C	0	-2.636134	0.00114	0.558103	0.54093	ENSG00000236104	ENST00000418724;ENST00000431845	T;T	0.04234	3.67;3.67	3.88	3.0	0.34707	.	.	.	.	.	T	0.00440	0.0014	N	0.02011	-0.69	0.54753	P	1.0999999999983245E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.45469	-0.9259	8	0.05620	T	0.96	.	5.3554	0.16057	0.0:0.6798:0.206:0.1142	rs3130100;rs17856567;rs57230775;rs3130100	310	O15209	ZBT22_HUMAN	A	310	ENSP00000404403:T310A;ENSP00000407545:T310A	ENSP00000404403:T310A	T	-	1	0	ZBTB22	33391744	1.000000	0.71417	0.563000	0.28383	0.381000	0.30169	1.935000	0.40173	0.327000	0.23409	-1.568000	0.00874	ACA	T|0.467;C|0.533	0.533	strong		0.567	ZBTB22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076183.2		
SLC22A16	85413	hgsc.bcm.edu	37	6	110763875	110763875	+	Missense_Mutation	SNP	A	A	G	rs723685	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr6:110763875A>G	ENST00000368919.3	-	4	821	c.755T>C	c.(754-756)gTt>gCt	p.V252A	RN7SL617P_ENST00000485298.2_RNA|SLC22A16_ENST00000330550.4_Missense_Mutation_p.V218A|SLC22A16_ENST00000456137.2_3'UTR|SLC22A16_ENST00000439654.1_Missense_Mutation_p.V252A	NM_033125.3	NP_149116.2	Q86VW1	S22AG_HUMAN	solute carrier family 22 (organic cation/carnitine transporter), member 16	252			V -> A (in dbSNP:rs723685).		acid secretion (GO:0046717)|amine transport (GO:0015837)|carnitine transmembrane transport (GO:1902603)|carnitine transport (GO:0015879)|cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|organic cation transport (GO:0015695)|single fertilization (GO:0007338)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	amine transmembrane transporter activity (GO:0005275)|carnitine transmembrane transporter activity (GO:0015226)|organic cation transmembrane transporter activity (GO:0015101)			breast(1)|endometrium(1)|kidney(3)|large_intestine(6)|lung(16)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	34		all_cancers(87;0.00221)|Acute lymphoblastic leukemia(125;2.27e-07)|all_hematologic(75;1.38e-05)|all_epithelial(87;0.0485)|Colorectal(196;0.101)		OV - Ovarian serous cystadenocarcinoma(136;0.0513)|Epithelial(106;0.0921)|all cancers(137;0.115)	Doxorubicin(DB00997)|L-Carnitine(DB00583)	CAGGGTTCCAACTGCAAAAAA	0.498													A|||	441	0.0880591	0.0968	0.1081	5008	,	,		18484	0.0794		0.0944	False		,,,				2504	0.0644				p.V252A		Atlas-SNP	.											.	SLC22A16	81	.	0			c.T755C						PASS	.	A	ALA/VAL	514,3892	236.5+/-248.6	22,470,1711	90.0	88.0	89.0		755	3.7	0.2	6	dbSNP_86	89	758,7842	181.0+/-229.8	33,692,3575	yes	missense	SLC22A16	NM_033125.2	64	55,1162,5286	GG,GA,AA		8.814,11.6659,9.7801	benign	252/578	110763875	1272,11734	2203	4300	6503	SO:0001583	missense	85413	exon4			GTTCCAACTGCAA		CCDS5084.1	6q21	2013-05-22	2008-01-11		ENSG00000004809	ENSG00000004809		"""Solute carriers"""	20302	protein-coding gene	gene with protein product		608276	"""solute carrier family 22 (organic cation transporter), member 16"""			12372408, 12089149, 17473959	Standard	NM_033125		Approved	FLIPT2, CT2, OKB1, OAT6	uc003puf.3	Q86VW1	OTTHUMG00000016171	ENST00000368919.3:c.755T>C	6.37:g.110763875A>G	ENSP00000357915:p.Val252Ala	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	63	6	0.0952381	NM_033125	O14567|Q5JXM1|Q8IUG8|Q8IZD5|Q96M90|Q96RU0	Missense_Mutation	SNP	ENST00000368919.3	37	CCDS5084.1	180	0.08241758241758242	43	0.08739837398373984	32	0.08839779005524862	39	0.06818181818181818	66	0.0870712401055409	A	9.846	1.192480	0.21954	0.116659	0.08814	ENSG00000004809	ENST00000368919;ENST00000451557;ENST00000330550;ENST00000439654;ENST00000434949;ENST00000437378	T;T;T;T;T;T	0.59772	0.24;0.24;0.24;0.24;0.24;0.24	4.84	3.67	0.42095	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.841724	0.10529	N	0.664036	T	0.33789	0.0875	L	0.52759	1.655	0.09310	P	1.0	B;B	0.10296	0.001;0.003	B;B	0.09377	0.004;0.003	T	0.15665	-1.0429	9	0.51188	T	0.08	.	10.5063	0.44836	0.9225:0.0:0.0775:0.0	rs723685;rs52815010;rs59277963;rs723685	252;218	Q86VW1;Q86VW1-2	S22AG_HUMAN;.	A	252;169;218;252;82;209	ENSP00000357915:V252A;ENSP00000395642:V169A;ENSP00000328583:V218A;ENSP00000408799:V252A;ENSP00000409306:V82A;ENSP00000416310:V209A	ENSP00000328583:V218A	V	-	2	0	SLC22A16	110870568	0.841000	0.29509	0.161000	0.22692	0.030000	0.12068	4.650000	0.61440	0.695000	0.31675	-0.264000	0.10439	GTT	A|0.905;G|0.095	0.095	strong		0.498	SLC22A16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043428.1	NM_033125	
MSH3	4437	hgsc.bcm.edu	37	5	79950708	79950708	+	Silent	SNP	T	T	C	rs201874762|rs2405875	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr5:79950708T>C	ENST00000265081.6	+	1	242	c.162T>C	c.(160-162)gcT>gcC	p.A54A	DHFR_ENST00000504396.1_5'Flank|DHFR_ENST00000513048.1_5'Flank|DHFR_ENST00000505337.1_5'Flank|DHFR_ENST00000511032.1_5'Flank|DHFR_ENST00000439211.2_5'UTR	NM_002439.4	NP_002430.3	P20585	MSH3_HUMAN	mutS homolog 3	54	Poly-Ala.				ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)|maintenance of DNA repeat elements (GO:0043570)|meiotic mismatch repair (GO:0000710)|mismatch repair (GO:0006298)|negative regulation of DNA recombination (GO:0045910)|positive regulation of helicase activity (GO:0051096)|reciprocal meiotic recombination (GO:0007131)|somatic recombination of immunoglobulin gene segments (GO:0016447)	membrane (GO:0016020)|MutSbeta complex (GO:0032302)|nuclear chromosome (GO:0000228)|nucleus (GO:0005634)	ATP binding (GO:0005524)|centromeric DNA binding (GO:0019237)|damaged DNA binding (GO:0003684)|DNA-dependent ATPase activity (GO:0008094)|double-strand/single-strand DNA junction binding (GO:0000406)|enzyme binding (GO:0019899)|heteroduplex DNA loop binding (GO:0000404)|Y-form DNA binding (GO:0000403)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(12)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	29		Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244)		OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33)		CTgcagcggctgcagcggccg	0.687								Mismatch excision repair (MMR)					-|||	259	0.0517173	0.0499	0.0447	5008	,	,		6179	0.0754		0.0437	False		,,,				2504	0.0429				p.A54A	Melanoma(88;1010 1399 13793 26548 36275)	Atlas-SNP	.											.	MSH3	129	.	0			c.T162C						PASS	.						9.0	9.0	9.0					5																	79950708		2150	4207	6357	SO:0001819	synonymous_variant	4437	exon1			AGCGGCTGCAGCG	U61981	CCDS34195.1	5q11-q12	2013-09-12	2013-09-12		ENSG00000113318	ENSG00000113318			7326	protein-coding gene	gene with protein product	"""Divergent upstream protein"", ""Mismatch repair protein 1"""	600887	"""mutS (E. coli) homolog 3"", ""mutS homolog 3 (E. coli)"""				Standard	NM_002439		Approved	DUP, MRP1	uc003kgz.4	P20585	OTTHUMG00000162540	ENST00000265081.6:c.162T>C	5.37:g.79950708T>C		Somatic	11	0	0		WXS	Illumina HiSeq	Phase_I	29	22	0.758621	NM_002439	A1L480|A1L482|A6NMM6|Q6PJT5|Q86UQ6|Q92867	Silent	SNP	ENST00000265081.6	37	CCDS34195.1																																																																																			T|0.781;C|0.219	0.219	strong		0.687	MSH3-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369471.1	NM_002439	
MUC4	4585	hgsc.bcm.edu	37	3	195511142	195511142	+	Missense_Mutation	SNP	T	T	C	rs430037	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr3:195511142T>C	ENST00000463781.3	-	2	7768	c.7309A>G	c.(7309-7311)Aac>Gac	p.N2437D	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.N2437D	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.N2437D(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)		GAGGAAACGTTGGTGACAGGA	0.597													.|||	2741	0.547324	0.4629	0.4841	5008	,	,		18811	0.75		0.5755	False		,,,				2504	0.4683				p.N2437D		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	1	Substitution - Missense(1)	prostate(1)	c.A7309G						scavenged	.						59.0	58.0	58.0					3																	195511142		645	1581	2226	SO:0001583	missense	4585	exon2			AAACGTTGGTGAC	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.7309A>G	3.37:g.195511142T>C	ENSP00000417498:p.Asn2437Asp	Somatic	64	1	0.015625		WXS	Illumina HiSeq	Phase_I	92	7	0.076087	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	.	.	.	.	.	.	.	.	.	.	T	6.228	0.410269	0.11812	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.34667	1.36;1.35	.	.	.	.	.	.	.	.	T	0.14917	0.0360	N	0.08118	0	0.09310	N	1	B	0.15141	0.012	B	0.04013	0.001	T	0.26950	-1.0088	7	.	.	.	.	3.8346	0.08888	0.0:0.0:0.3913:0.6087	.	2437	E7ESK3	.	D	2437	ENSP00000417498:N2437D;ENSP00000420243:N2437D	.	N	-	1	0	MUC4	196995537	.	.	0.023000	0.16930	0.000000	0.00434	.	.	0.402000	0.25451	0.000000	0.15137	AAC	T|0.781;C|0.219	0.219	strong		0.597	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
OR51A2	401667	hgsc.bcm.edu	37	11	4976291	4976291	+	Missense_Mutation	SNP	G	G	A	rs55889636	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr11:4976291G>A	ENST00000380371.1	-	1	652	c.653C>T	c.(652-654)tCt>tTt	p.S218F	MMP26_ENST00000477339.1_Intron|MMP26_ENST00000380390.1_Intron	NM_001004748.1	NP_001004748.1	Q8NGJ7	O51A2_HUMAN	olfactory receptor, family 51, subfamily A, member 2	218						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(1)|large_intestine(3)|lung(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	17		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)		CAGGGTGTAAGACACAGCAAT	0.428													.|||	1878	0.375	0.3722	0.3905	5008	,	,		14851	0.379		0.4841	False		,,,				2504	0.2515				p.S218F		Atlas-SNP	.											OR51A2,NS,carcinoma,0,1	OR51A2	40	1	0			c.C653T						scavenged	.		PHE/SER	1533,2741		432,669,1036	80.0	62.0	68.0		653	3.1	0.1	11	dbSNP_129	68	3770,4262		1350,1070,1596	yes	missense	OR51A2	NM_001004748.1	155	1782,1739,2632	AA,AG,GG		46.9373,35.868,43.0928	probably-damaging	218/314	4976291	5303,7003	2137	4016	6153	SO:0001583	missense	401667	exon1			GTGTAAGACACAG	AB065797	CCDS31368.1	11p15.4	2012-08-09			ENSG00000205496	ENSG00000205496		"""GPCR / Class A : Olfactory receptors"""	14764	protein-coding gene	gene with protein product							Standard	NM_001004748		Approved		uc010qyt.2	Q8NGJ7	OTTHUMG00000066602	ENST00000380371.1:c.653C>T	11.37:g.4976291G>A	ENSP00000369729:p.Ser218Phe	Somatic	525	0	0		WXS	Illumina HiSeq	Phase_I	516	5	0.00968992	NM_001004748		Missense_Mutation	SNP	ENST00000380371.1	37	CCDS31368.1	802	0.36721611721611724	148	0.3008130081300813	117	0.32320441988950277	194	0.33916083916083917	343	0.4525065963060686	-	16.73	3.204617	0.58234	0.35868	0.469373	ENSG00000205496	ENST00000380371	T	0.42513	0.97	3.13	3.13	0.36017	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00012	0.0000	H	0.96208	3.785	0.32076	P	0.5937319999999999	D	0.89917	1.0	D	0.97110	1.0	T	0.42224	-0.9464	8	0.87932	D	0	.	13.3431	0.60555	0.0:0.0:1.0:0.0	rs55889636	218	Q8NGJ7	O51A2_HUMAN	F	218	ENSP00000369729:S218F	ENSP00000369729:S218F	S	-	2	0	OR51A2	4932867	0.998000	0.40836	0.057000	0.19452	0.032000	0.12392	5.391000	0.66266	1.757000	0.51966	0.395000	0.25975	TCT	G|0.661;A|0.339	0.339	strong		0.428	OR51A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142809.1	NM_001004748	
FANCA	2175	hgsc.bcm.edu	37	16	89866043	89866043	+	Missense_Mutation	SNP	T	T	C	rs7190823	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr16:89866043T>C	ENST00000389301.3	-	9	826	c.796A>G	c.(796-798)Acg>Gcg	p.T266A	FANCA_ENST00000543736.1_Missense_Mutation_p.T234A|FANCA_ENST00000534992.1_Missense_Mutation_p.T266A|FANCA_ENST00000563673.1_Missense_Mutation_p.T266A|FANCA_ENST00000568369.1_Missense_Mutation_p.T266A|FANCA_ENST00000389302.3_Missense_Mutation_p.T266A	NM_000135.2	NP_000126.2	O15360	FANCA_HUMAN	Fanconi anemia, complementation group A	266			T -> A (in dbSNP:rs7190823). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:18987736, ECO:0000269|PubMed:9399890, ECO:0000269|Ref.4}.		DNA repair (GO:0006281)|female gonad development (GO:0008585)|male gonad development (GO:0008584)|male meiosis (GO:0007140)|protein complex assembly (GO:0006461)|regulation of cell proliferation (GO:0042127)	cytoplasm (GO:0005737)|Fanconi anaemia nuclear complex (GO:0043240)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(5)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(16)|ovary(3)|skin(2)|urinary_tract(3)	47		Lung NSC(15;8.48e-06)|all_lung(18;1.31e-05)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.028)		ACATCAACCGTGACCTGTCAA	0.358			"""D, Mis, N, F, S"""			"""AML, leukemia"""		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia				C|||	3458	0.690495	0.7625	0.6037	5008	,	,		21218	0.9871		0.3956	False		,,,				2504	0.6524				p.T266A		Atlas-SNP	.	yes	Rec		Fanconi anaemia A	16	16q24.3	2175	"""Fanconi anemia, complementation group A"""		L	FANCA,colon,carcinoma,+1,1	FANCA	99	1	0			c.A796G						scavenged	.	C	ALA/THR,ALA/THR	3190,1206	421.5+/-339.4	1151,888,159	147.0	127.0	134.0		796,796	1.9	0.1	16	dbSNP_116	134	3386,5214	640.8+/-399.6	677,2032,1591	yes	missense,missense	FANCA	NM_000135.2,NM_001018112.1	58,58	1828,2920,1750	CC,CT,TT		39.3721,27.434,49.3998	benign,benign	266/1456,266/298	89866043	6576,6420	2198	4300	6498	SO:0001583	missense	2175	exon9	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	CAACCGTGACCTG	Z83067	CCDS32515.1, CCDS42221.1, CCDS67099.1	16q24.3	2014-09-17			ENSG00000187741	ENSG00000187741		"""Fanconi anemia, complementation groups"""	3582	protein-coding gene	gene with protein product		607139		FACA, FANCH		7581462, 9382107	Standard	NM_001286167		Approved	FAA, FA-H, FAH	uc002fou.1	O15360		ENST00000389301.3:c.796A>G	16.37:g.89866043T>C	ENSP00000373952:p.Thr266Ala	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	108	4	0.037037	NM_000135	A5D923|B4DRI7|H3BSR5|O75266|Q6PL10|Q92497|Q96H18|Q9UEA5|Q9UEL8|Q9UEL9|Q9UPK3|Q9Y6M2	Missense_Mutation	SNP	ENST00000389301.3	37	CCDS32515.1	1435	0.657051282051282	370	0.7520325203252033	199	0.5497237569060773	564	0.986013986013986	302	0.39841688654353563	C	0.399	-0.919409	0.02396	0.72566	0.393721	ENSG00000187741	ENST00000389301;ENST00000389302;ENST00000534992;ENST00000543736	T;T;T;T	0.37584	1.19;1.19;1.19;1.19	4.1	1.85	0.25348	.	0.674836	0.13063	N	0.416735	T	0.00012	0.0000	N	0.00162	-1.95	0.80722	P	0.0	B;B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0;0.0	B;B;B;B;B;B	0.01281	0.0;0.0;0.0;0.0;0.0;0.0	T	0.29397	-1.0013	9	0.02654	T	1	-13.3596	5.1091	0.14800	0.4757:0.4147:0.0:0.1096	rs7190823;rs17232400;rs17669765;rs52833740;rs57464202;rs7190823	266;234;266;266;266;266	B4DRI7;Q0VAP4;A0PJU8;F5H8D5;O15360-2;O15360	.;.;.;.;.;FANCA_HUMAN	A	266;266;266;234	ENSP00000373952:T266A;ENSP00000373953:T266A;ENSP00000443675:T266A;ENSP00000443409:T234A	ENSP00000373952:T266A	T	-	1	0	FANCA	88393544	0.007000	0.16637	0.078000	0.20375	0.146000	0.21551	0.402000	0.20965	0.381000	0.24851	-0.222000	0.12452	ACG	T|0.408;C|0.592	0.592	strong		0.358	FANCA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000421927.1		
TNRC6C	57690	hgsc.bcm.edu	37	17	76063864	76063864	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr17:76063864G>A	ENST00000588061.1	+	7	3365	c.2638G>A	c.(2638-2640)Ggc>Agc	p.G880S	RNU6-625P_ENST00000459412.1_RNA|TNRC6C_ENST00000544502.1_Missense_Mutation_p.G877S|TNRC6C_ENST00000335749.4_Missense_Mutation_p.G877S|TNRC6C_ENST00000541771.1_Missense_Mutation_p.G880S|TNRC6C_ENST00000588847.1_Missense_Mutation_p.G877S|TNRC6C_ENST00000301624.4_Missense_Mutation_p.G880S			Q9HCJ0	TNR6C_HUMAN	trinucleotide repeat containing 6C	880	Sufficient for interaction with argonaute family proteins.				embryonic hemopoiesis (GO:0035162)|endoderm formation (GO:0001706)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|innate immune response (GO:0045087)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|regulation of gene silencing by miRNA (GO:0060964)	cytosol (GO:0005829)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(9)|lung(16)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	40			BRCA - Breast invasive adenocarcinoma(99;0.00269)|Lung(188;0.0973)			AGAAGGCTGGGGCAGTGGTGG	0.463																																					p.G880S		Atlas-SNP	.											.	TNRC6C	173	.	0			c.G2638A						PASS	.						127.0	129.0	128.0					17																	76063864		1937	4151	6088	SO:0001583	missense	57690	exon6			GGCTGGGGCAGTG	AL834429	CCDS45798.1, CCDS45799.1	17q25.3	2012-10-04			ENSG00000078687	ENSG00000078687		"""Trinucleotide (CAG) repeat containing"""	29318	protein-coding gene	gene with protein product		610741					Standard	NM_018996		Approved	KIAA1582, FLJ20015	uc002juf.2	Q9HCJ0	OTTHUMG00000132642	ENST00000588061.1:c.2638G>A	17.37:g.76063864G>A	ENSP00000468647:p.Gly880Ser	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	81	4	0.0493827	NM_018996	G3XAB8|Q86UE5|Q8N3D8|Q96MU9	Missense_Mutation	SNP	ENST00000588061.1	37	CCDS45798.1	.	.	.	.	.	.	.	.	.	.	G	35	5.459818	0.96240	.	.	ENSG00000078687	ENST00000455761;ENST00000395801;ENST00000335749;ENST00000301624;ENST00000541771;ENST00000544502	T;T;T;T	0.17054	2.3;2.33;2.33;2.3	5.84	5.84	0.93424	Argonaute hook domain (1);	0.000000	0.85682	D	0.000000	T	0.44932	0.1317	M	0.74647	2.275	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;0.999;1.0	T	0.07654	-1.0761	10	0.32370	T	0.25	-20.2912	20.1187	0.97949	0.0:0.0:1.0:0.0	.	877;880;880	G3XAB8;Q9HCJ0-2;Q9HCJ0	.;.;TNR6C_HUMAN	S	880;877;877;880;880;877	ENSP00000336783:G877S;ENSP00000301624:G880S;ENSP00000440310:G880S;ENSP00000442421:G877S	ENSP00000301624:G880S	G	+	1	0	TNRC6C	73575459	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.420000	0.97426	2.767000	0.95098	0.591000	0.81541	GGC	.	.	none		0.463	TNRC6C-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000395947.1	NM_018996	
ZNF614	80110	hgsc.bcm.edu	37	19	52519608	52519608	+	Missense_Mutation	SNP	C	C	T	rs8104890	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr19:52519608C>T	ENST00000270649.6	-	5	1787	c.1243G>A	c.(1243-1245)Gtt>Att	p.V415I	ZNF614_ENST00000356322.6_Intron	NM_025040.3	NP_079316.2	Q8N883	ZN614_HUMAN	zinc finger protein 614	415			V -> I (in dbSNP:rs8104890).		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)|kidney(1)|large_intestine(6)|lung(9)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	24		all_neural(266;0.0505)		GBM - Glioblastoma multiforme(134;0.00513)|OV - Ovarian serous cystadenocarcinoma(262;0.0177)		TGATGTATAACGAGAGTGCGT	0.428													T|||	2020	0.403355	0.3797	0.3444	5008	,	,		23869	0.4038		0.2773	False		,,,				2504	0.6063				p.V415I		Atlas-SNP	.											.	ZNF614	58	.	0			c.G1243A						PASS	.	T	ILE/VAL	1675,2731	655.4+/-399.9	320,1035,848	173.0	169.0	170.0		1243	-0.1	0.0	19	dbSNP_116	170	2291,6309	705.9+/-405.5	295,1701,2304	yes	missense	ZNF614	NM_025040.3	29	615,2736,3152	TT,TC,CC		26.6395,38.0163,30.4936	benign	415/586	52519608	3966,9040	2203	4300	6503	SO:0001583	missense	80110	exon5			GTATAACGAGAGT	BC022246	CCDS12847.1	19q13.41	2013-01-08				ENSG00000142556		"""Zinc fingers, C2H2-type"", ""-"""	24722	protein-coding gene	gene with protein product						12477932	Standard	NM_025040		Approved	FLJ21941	uc002pyj.3	Q8N883		ENST00000270649.6:c.1243G>A	19.37:g.52519608C>T	ENSP00000270649:p.Val415Ile	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	89	4	0.0449438	NM_025040	Q494T8|Q8TCF4|Q9BSN8	Missense_Mutation	SNP	ENST00000270649.6	37	CCDS12847.1	742	0.33974358974358976	199	0.40447154471544716	119	0.3287292817679558	206	0.36013986013986016	218	0.287598944591029	T	0.148	-1.094924	0.01858	0.380163	0.266395	ENSG00000142556	ENST00000270649	T	0.07567	3.18	3.5	-0.11	0.13580	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.16478	0.41	0.80722	P	0.0	B	0.11235	0.004	B	0.06405	0.002	T	0.45833	-0.9234	8	0.02654	T	1	.	4.0797	0.09921	0.1457:0.2773:0.0:0.577	rs8104890;rs17743253;rs52816123;rs60685404;rs8104890	415	Q8N883	ZN614_HUMAN	I	415	ENSP00000270649:V415I	ENSP00000270649:V415I	V	-	1	0	ZNF614	57211420	0.000000	0.05858	0.000000	0.03702	0.857000	0.48899	-1.520000	0.02241	-0.247000	0.09597	-1.216000	0.01612	GTT	C|0.666;T|0.334	0.334	strong		0.428	ZNF614-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462407.1	NM_025040	
FAM76A	199870	hgsc.bcm.edu	37	1	28060574	28060574	+	Silent	SNP	A	A	G	rs6670793	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr1:28060574A>G	ENST00000373954.6	+	4	336	c.234A>G	c.(232-234)gcA>gcG	p.A78A	FAM76A_ENST00000530324.1_Silent_p.A78A|FAM76A_ENST00000010299.6_Silent_p.A112A|FAM76A_ENST00000234549.7_Silent_p.A112A|FAM76A_ENST00000373949.1_Silent_p.A78A|FAM76A_ENST00000419687.2_Intron	NM_001143912.1|NM_152660.2	NP_001137384.1|NP_689873.1	Q8TAV0	FA76A_HUMAN	family with sequence similarity 76, member A	78										endometrium(4)|kidney(2)|large_intestine(1)|lung(2)	9		Colorectal(325;0.000147)|all_lung(284;0.00181)|Lung NSC(340;0.00278)|Renal(390;0.00357)|Breast(348;0.0115)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0545)|all_neural(195;0.0966)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0429)|OV - Ovarian serous cystadenocarcinoma(117;3.52e-24)|Colorectal(126;3.23e-08)|COAD - Colon adenocarcinoma(152;1.75e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00253)|KIRC - Kidney renal clear cell carcinoma(1967;0.00292)|STAD - Stomach adenocarcinoma(196;0.00308)|READ - Rectum adenocarcinoma(331;0.0649)		ACATAATTGCAGCATTTATTG	0.373													G|||	1267	0.252995	0.6241	0.0865	5008	,	,		17697	0.2669		0.0149	False		,,,				2504	0.1002				p.A112A		Atlas-SNP	.											.	FAM76A	11	.	0			c.A336G						PASS	.	G	,,,,	2259,2147	578.5+/-384.7	579,1101,523	81.0	86.0	84.0		336,336,234,,234	-9.3	0.5	1	dbSNP_116	84	136,8464	813.4+/-407.0	1,134,4165	no	coding-synonymous,coding-synonymous,coding-synonymous,intron,coding-synonymous	FAM76A	NM_001143912.1,NM_001143913.1,NM_001143914.1,NM_001143915.1,NM_152660.2	,,,,	580,1235,4688	GG,GA,AA		1.5814,48.729,18.4146	,,,,	112/342,112/313,78/279,,78/308	28060574	2395,10611	2203	4300	6503	SO:0001819	synonymous_variant	199870	exon5			AATTGCAGCATTT	AK098318	CCDS309.1, CCDS44092.1, CCDS44093.1, CCDS44094.1, CCDS44095.1	1p35.3	2008-02-05			ENSG00000009780	ENSG00000009780			28530	protein-coding gene	gene with protein product							Standard	NM_001143912		Approved	MGC34648	uc001bor.3	Q8TAV0	OTTHUMG00000003729	ENST00000373954.6:c.234A>G	1.37:g.28060574A>G		Somatic	219	0	0		WXS	Illumina HiSeq	Phase_I	222	9	0.0405405	NM_001143912	B4DWT3|O95565|O95566|Q8N7J5	Silent	SNP	ENST00000373954.6	37	CCDS309.1																																																																																			A|0.789;G|0.211	0.211	strong		0.373	FAM76A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000010514.3	NM_152660	
PTAFR	5724	hgsc.bcm.edu	37	1	28476862	28476862	+	Missense_Mutation	SNP	G	G	T	rs5938	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr1:28476862G>T	ENST00000373857.3	-	2	1305	c.671C>A	c.(670-672)gCt>gAt	p.A224D	PTAFR_ENST00000539896.1_Missense_Mutation_p.A224D|PTAFR_ENST00000305392.3_Missense_Mutation_p.A224D	NM_000952.4|NM_001164722.2|NM_001164723.2	NP_000943.1|NP_001158194.1|NP_001158195.1	P25105	PTAFR_HUMAN	platelet-activating factor receptor	224			A -> D (in dbSNP:rs5938). {ECO:0000269|PubMed:10391209}.		chemotaxis (GO:0006935)|cytokine production (GO:0001816)|cytokine-mediated signaling pathway (GO:0019221)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|inflammatory response (GO:0006954)|inositol trisphosphate biosynthetic process (GO:0032959)|interferon-gamma-mediated signaling pathway (GO:0060333)|phosphatidylinositol-mediated signaling (GO:0048015)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|lipopolysaccharide binding (GO:0001530)|lipopolysaccharide receptor activity (GO:0001875)|phospholipid binding (GO:0005543)|platelet activating factor receptor activity (GO:0004992)	p.A224D(1)		NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(8)|stomach(1)	15		Colorectal(325;0.000147)|Renal(390;0.00357)|Lung NSC(340;0.00715)|all_lung(284;0.00732)|Breast(348;0.0174)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0545)|all_neural(195;0.0557)		UCEC - Uterine corpus endometrioid carcinoma (279;0.215)|OV - Ovarian serous cystadenocarcinoma(117;6e-22)|Colorectal(126;3.04e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00279)|BRCA - Breast invasive adenocarcinoma(304;0.00595)|STAD - Stomach adenocarcinoma(196;0.00678)|READ - Rectum adenocarcinoma(331;0.0649)		CTTGACTTCAGCGTTGCGCTG	0.592													G|||	119	0.023762	0.0	0.0	5008	,	,		22009	0.1151		0.0	False		,,,				2504	0.0031				p.A224D		Atlas-SNP	.											PTAFR,NS,carcinoma,0,1	PTAFR	30	1	1	Substitution - Missense(1)	stomach(1)	c.C671A	GRCh37	CM016130	PTAFR	M	rs5938	scavenged	.	G	ASP/ALA,ASP/ALA,ASP/ALA,ASP/ALA	2,4404	4.2+/-10.8	0,2,2201	69.0	60.0	63.0		671,671,671,671	3.5	0.0	1	dbSNP_52	63	0,8600		0,0,4300	yes	missense,missense,missense,missense	PTAFR	NM_000952.4,NM_001164721.1,NM_001164722.2,NM_001164723.2	126,126,126,126	0,2,6501	TT,TG,GG		0.0,0.0454,0.0154	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	224/343,224/343,224/343,224/343	28476862	2,13004	2203	4300	6503	SO:0001583	missense	5724	exon3			ACTTCAGCGTTGC	BC063000	CCDS318.1	1p35-p34.3	2012-08-20			ENSG00000169403	ENSG00000169403		"""GPCR / Class A : Platelet-activating factor receptors"""	9582	protein-coding gene	gene with protein product		173393				1322356	Standard	NM_001164721		Approved		uc001bpl.3	P25105	OTTHUMG00000003953	ENST00000373857.3:c.671C>A	1.37:g.28476862G>T	ENSP00000362965:p.Ala224Asp	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	110	4	0.0363636	NM_001164723	A3KMC8|A8K2H5	Missense_Mutation	SNP	ENST00000373857.3	37	CCDS318.1	62	0.028388278388278388	0	0.0	0	0.0	62	0.10839160839160839	0	0.0	G	14.60	2.582638	0.46006	4.54E-4	0.0	ENSG00000169403	ENST00000373857;ENST00000539896;ENST00000305392	T;T;T	0.48836	0.8;0.8;0.8	5.38	3.51	0.40186	GPCR, rhodopsin-like superfamily (1);	0.382363	0.28409	N	0.015452	T	0.01287	0.0042	L	0.38838	1.175	0.09310	N	1	P	0.34615	0.459	P	0.48738	0.588	T	0.02378	-1.1168	10	0.42905	T	0.14	.	10.8858	0.46965	0.1525:0.0:0.8475:0.0	rs5938;rs3738164;rs5938	224	P25105	PTAFR_HUMAN	D	224	ENSP00000362965:A224D;ENSP00000442658:A224D;ENSP00000301974:A224D	ENSP00000301974:A224D	A	-	2	0	PTAFR	28349449	0.025000	0.19082	0.004000	0.12327	0.831000	0.47069	1.866000	0.39489	0.645000	0.30675	0.563000	0.77884	GCT	G|0.968;T|0.030	0.030	strong		0.592	PTAFR-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011258.1	NM_000952	
DOK3	79930	hgsc.bcm.edu	37	5	176936819	176936819	+	Missense_Mutation	SNP	C	C	G	rs3749728	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr5:176936819C>G	ENST00000357198.4	-	1	39	c.35G>C	c.(34-36)cGt>cCt	p.R12P	DOK3_ENST00000312943.6_Intron|DOK3_ENST00000377112.4_Intron|DOK3_ENST00000501403.2_Intron	NM_024872.2	NP_079148.2	Q7L591	DOK3_HUMAN	docking protein 3	12			R -> P (in dbSNP:rs3749728).		Ras protein signal transduction (GO:0007265)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)				NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|lung(7)	13	all_cancers(89;0.00033)|Renal(175;0.000269)|Lung NSC(126;0.00161)|all_lung(126;0.00286)	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)|Epithelial(233;0.191)			CAGCTGGGCACGCGCGTCTGA	0.711													C|||	734	0.146565	0.2466	0.098	5008	,	,		12252	0.1677		0.0517	False		,,,				2504	0.1217				p.R12P		Atlas-SNP	.											.	DOK3	41	.	0			c.G35C						PASS	.	C	,,PRO/ARG	783,3621	294.4+/-283.1	73,637,1492	52.0	52.0	52.0		,,35	-1.2	0.0	5	dbSNP_107	52	456,8144	133.1+/-190.7	6,444,3850	yes	intron,intron,missense	DOK3	NM_001144875.1,NM_001144876.1,NM_024872.2	,,103	79,1081,5342	GG,GC,CC		5.3023,17.7793,9.5278	,,benign	,,12/497	176936819	1239,11765	2202	4300	6502	SO:0001583	missense	79930	exon1			TGGGCACGCGCGT	AK026223	CCDS4426.1, CCDS47349.1, CCDS47350.1	5q35	2008-02-05			ENSG00000146094	ENSG00000146094			24583	protein-coding gene	gene with protein product		611435				10733577, 12595900	Standard	NM_024872		Approved	FLJ22570	uc003mhk.3	Q7L591	OTTHUMG00000130850	ENST00000357198.4:c.35G>C	5.37:g.176936819C>G	ENSP00000349727:p.Arg12Pro	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	161	9	0.0559006	NM_024872	E9PAT0|H7BXS0|Q8N864|Q9BQB3|Q9H666	Missense_Mutation	SNP	ENST00000357198.4	37	CCDS4426.1	307	0.14056776556776557	120	0.24390243902439024	29	0.08011049723756906	113	0.19755244755244755	45	0.059366754617414245	C	1.719	-0.497217	0.04291	0.177793	0.053023	ENSG00000146094	ENST00000357198	T	0.21191	2.02	2.88	-1.2	0.09554	.	4.401390	0.01202	U	0.007607	T	0.00012	0.0000	N	0.08118	0	0.58432	P	5.999999999950489E-6	B	0.24483	0.104	B	0.17979	0.02	T	0.37572	-0.9700	9	0.87932	D	0	.	6.1537	0.20326	0.0:0.2892:0.0:0.7108	rs3749728;rs60122350;rs3749728	12	Q7L591	DOK3_HUMAN	P	12	ENSP00000349727:R12P	ENSP00000349727:R12P	R	-	2	0	DOK3	176869425	0.000000	0.05858	0.001000	0.08648	0.004000	0.04260	-0.285000	0.08410	-0.168000	0.10853	-1.629000	0.00783	CGT	C|0.892;G|0.108	0.108	strong		0.711	DOK3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000253420.4	NM_024872	
NOSTRIN	115677	hgsc.bcm.edu	37	2	169681151	169681151	+	Silent	SNP	C	C	T	rs3732031	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr2:169681151C>T	ENST00000317647.7	+	3	350	c.121C>T	c.(121-123)Ctg>Ttg	p.L41L	NOSTRIN_ENST00000421711.2_Intron|NOSTRIN_ENST00000397206.2_5'UTR|NOSTRIN_ENST00000444448.2_Silent_p.L41L|NOSTRIN_ENST00000445023.2_5'UTR|NOSTRIN_ENST00000397209.2_Intron|NOSTRIN_ENST00000458381.2_Silent_p.L41L	NM_001039724.3	NP_001034813.2	Q8IVI9	NOSTN_HUMAN	nitric oxide synthase trafficking	41	FCH. {ECO:0000255|PROSITE- ProRule:PRU00083}.				endocytosis (GO:0006897)|negative regulation of transcription, DNA-templated (GO:0045892)|nitric oxide metabolic process (GO:0046209)|regulation of nitric-oxide synthase activity (GO:0050999)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytoskeleton (GO:0005856)|endocytic vesicle membrane (GO:0030666)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)	p.L41L(2)		kidney(1)|large_intestine(1)|lung(4)|prostate(1)|skin(1)|urinary_tract(1)	9						CAGGGCAAACCTGGAAATTAG	0.473													C|||	535	0.106829	0.0446	0.0576	5008	,	,		21300	0.2788		0.0308	False		,,,				2504	0.1268				p.L41L		Atlas-SNP	.											NOSTRIN_ENST00000444448,NS,carcinoma,0,2	NOSTRIN	68	2	2	Substitution - coding silent(2)	prostate(2)	c.C121T						scavenged	.	C	,,,	140,3642		2,136,1753	82.0	77.0	79.0		121,121,,	3.2	1.0	2	dbSNP_107	79	273,7981		6,261,3860	no	coding-synonymous,coding-synonymous,intron,utr-5	NOSTRIN	NM_001039724.3,NM_001171631.1,NM_001171632.1,NM_052946.3	,,,	8,397,5613	TT,TC,CC		3.3075,3.7017,3.4314	,,,	41/507,41/564,,	169681151	413,11623	1891	4127	6018	SO:0001819	synonymous_variant	115677	exon3			GCAAACCTGGAAA	AJ532842	CCDS42771.1, CCDS42772.1, CCDS54415.1, CCDS54416.1	2q31.1	2013-08-05	2013-08-05		ENSG00000163072	ENSG00000163072			20203	protein-coding gene	gene with protein product		607496	"""nitric oxide synthase trafficker"""			12446846	Standard	NM_001171631		Approved	MGC20702	uc002ueg.3	Q8IVI9	OTTHUMG00000153990	ENST00000317647.7:c.121C>T	2.37:g.169681151C>T		Somatic	584	1	0.00171233		WXS	Illumina HiSeq	Phase_I	548	6	0.0109489	NM_001039724	A8K2I9|B3KSF5|E7EPT9|Q27HG3|Q53S62|Q96CJ9	Silent	SNP	ENST00000317647.7	37	CCDS42771.1																																																																																			C|0.900;T|0.100	0.100	strong		0.473	NOSTRIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333356.4	NM_052946	
SMARCAD1	56916	hgsc.bcm.edu	37	4	95186055	95186055	+	Silent	SNP	A	A	G	rs2306802	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr4:95186055A>G	ENST00000354268.4	+	10	1552	c.1479A>G	c.(1477-1479)caA>caG	p.Q493Q	SMARCAD1_ENST00000457823.2_Silent_p.Q493Q|SMARCAD1_ENST00000509418.1_Silent_p.Q63Q			Q9H4L7	SMRCD_HUMAN	SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a, containing DEAD/H box 1	493					ATP-dependent chromatin remodeling (GO:0043044)|chromatin modification (GO:0016568)|chromatin remodeling (GO:0006338)|chromosome separation (GO:0051304)|DNA double-strand break processing (GO:0000729)|histone H3 deacetylation (GO:0070932)|histone H4 deacetylation (GO:0070933)|nucleotide metabolic process (GO:0009117)|positive regulation of transcription, DNA-templated (GO:0045893)|protein homooligomerization (GO:0051260)|regulation of DNA recombination (GO:0000018)	heterochromatin (GO:0000792)|nuclear matrix (GO:0016363)|nuclear replication fork (GO:0043596)|nucleus (GO:0005634)|site of double-strand break (GO:0035861)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)	p.Q493Q(2)		breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(11)|liver(2)|lung(15)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	44				OV - Ovarian serous cystadenocarcinoma(123;4.33e-08)		TTCTAAACCAAAGGTAATCTT	0.308													A|||	1679	0.335264	0.0673	0.3501	5008	,	,		18015	0.499		0.3698	False		,,,				2504	0.4826				p.Q493Q		Atlas-SNP	.											SMARCAD1,NS,carcinoma,0,1	SMARCAD1	97	1	2	Substitution - coding silent(2)	prostate(2)	c.A1479G						scavenged	.	A	,,	546,3858	239.6+/-250.7	36,474,1692	53.0	51.0	52.0		1479,1479,1479	3.2	1.0	4	dbSNP_100	52	3266,5330	480.4+/-370.4	628,2010,1660	no	coding-synonymous,coding-synonymous,coding-synonymous	SMARCAD1	NM_001128429.1,NM_001128430.1,NM_020159.3	,,	664,2484,3352	GG,GA,AA		37.9944,12.3978,29.3231	,,	493/1029,493/1029,493/1027	95186055	3812,9188	2202	4298	6500	SO:0001819	synonymous_variant	56916	exon10			AAACCAAAGGTAA	AB032948	CCDS3639.1, CCDS47101.1, CCDS58914.1	4q22-q23	2008-02-05			ENSG00000163104	ENSG00000163104			18398	protein-coding gene	gene with protein product		612761				11031099	Standard	NM_001128430		Approved	ETL1, DKFZP762K2015, KIAA1122, DKFZp762K2015	uc003htb.4	Q9H4L7	OTTHUMG00000130971	ENST00000354268.4:c.1479A>G	4.37:g.95186055A>G		Somatic	442	3	0.00678733		WXS	Illumina HiSeq	Phase_I	400	10	0.025	NM_001128429	B7Z799|Q05D56|Q96SX1|Q9H017|Q9H860|Q9NPU9|Q9ULU7	Silent	SNP	ENST00000354268.4	37	CCDS3639.1																																																																																			A|0.691;G|0.309	0.309	strong		0.308	SMARCAD1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253583.1	NM_020159	
TNFRSF10C	8794	hgsc.bcm.edu	37	8	22974315	22974315	+	Missense_Mutation	SNP	A	A	C	rs61736405		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr8:22974315A>C	ENST00000356864.3	+	5	1083	c.551A>C	c.(550-552)aAc>aCc	p.N184T	TNFRSF10C_ENST00000540813.1_Missense_Mutation_p.N82T	NM_003841.3	NP_003832	O14798	TR10C_HUMAN	tumor necrosis factor receptor superfamily, member 10c, decoy without an intracellular domain	184					apoptotic process (GO:0006915)|signal transduction (GO:0007165)	anchored component of membrane (GO:0031225)|integral component of plasma membrane (GO:0005887)	transmembrane signaling receptor activity (GO:0004888)	p.N184T(1)		endometrium(1)|large_intestine(6)|lung(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	15		Prostate(55;0.0421)|Breast(100;0.067)		Colorectal(74;0.0147)|COAD - Colon adenocarcinoma(73;0.0612)		GAGACAATGAACACCAGCCCG	0.602																																					p.N184T		Atlas-SNP	.											TNFRSF10C,trunk,malignant_melanoma,0,1	TNFRSF10C	30	1	1	Substitution - Missense(1)	skin(1)	c.A551C						scavenged	.						68.0	80.0	76.0					8																	22974315		2203	4297	6500	SO:0001583	missense	8794	exon5			CAATGAACACCAG	AF012536	CCDS6037.1	8p22-p21	2006-02-22			ENSG00000173535	ENSG00000173535		"""Tumor necrosis factor receptor superfamily"", ""CD molecules"""	11906	protein-coding gene	gene with protein product		603613				9314565, 9325248	Standard	NM_003841		Approved	DcR1, TRAILR3, LIT, TRID, CD263	uc003xcy.3	O14798	OTTHUMG00000097844	ENST00000356864.3:c.551A>C	8.37:g.22974315A>C	ENSP00000349324:p.Asn184Thr	Somatic	128	8	0.0625		WXS	Illumina HiSeq	Phase_I	107	11	0.102804	NM_003841	O14755|Q08AS6|Q6FH98|Q6UXM5	Missense_Mutation	SNP	ENST00000356864.3	37	CCDS6037.1	.	.	.	.	.	.	.	.	.	.	A	1.881	-0.457883	0.04508	.	.	ENSG00000173535	ENST00000356864;ENST00000540813;ENST00000544885	T;T	0.62788	0.0;1.25	.	.	.	.	0.568776	0.17737	U	0.163718	T	0.28400	0.0702	N	0.03608	-0.345	0.22213	N	0.999289	P	0.38110	0.618	B	0.33690	0.168	T	0.14924	-1.0455	9	0.37606	T	0.19	.	2.8413	0.05530	0.5024:0.497:2.0E-4:3.0E-4	rs61736405	184	O14798	TR10C_HUMAN	T	184;82;184	ENSP00000349324:N184T;ENSP00000437612:N82T	ENSP00000349324:N184T	N	+	2	0	TNFRSF10C	23030260	0.001000	0.12720	0.054000	0.19295	0.104000	0.19210	0.918000	0.28678	0.077000	0.16863	0.076000	0.15429	AAC	A|0.013;C|0.987	0.987	weak		0.602	TNFRSF10C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215134.3		
OR4M2	390538	hgsc.bcm.edu	37	15	22368855	22368855	+	Missense_Mutation	SNP	T	T	C	rs75967710	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr15:22368855T>C	ENST00000332663.2	+	1	378	c.280T>C	c.(280-282)Ttt>Ctt	p.F94L	RP11-69H14.6_ENST00000558896.1_RNA	NM_001004719.2	NP_001004719.2	Q8NGB6	OR4M2_HUMAN	olfactory receptor, family 4, subfamily M, member 2	94						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(2)|endometrium(2)|kidney(4)|large_intestine(6)|lung(38)|ovary(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)	63		all_cancers(20;1.94e-20)|all_epithelial(15;3.94e-18)|Lung NSC(15;8.53e-15)|all_lung(15;2.87e-14)|Breast(32;0.00519)|Colorectal(260;0.101)	GBM - Glioblastoma multiforme(6;0.124)	all cancers(64;1.64e-11)|Epithelial(43;5.81e-10)|BRCA - Breast invasive adenocarcinoma(123;0.000255)|Kidney(6;0.00736)|KIRC - Kidney renal clear cell carcinoma(6;0.0135)|GBM - Glioblastoma multiforme(186;0.0963)		GATAATTTCTTTTGATGGATG	0.443																																					p.F94L		Atlas-SNP	.											.	OR4M2	140	.	0			c.T280C						PASS	.		LEU/PHE	54,4352		0,54,2149	327.0	277.0	294.0		280	2.5	0.9	15	dbSNP_131	294	111,8489		0,111,4189	yes	missense	OR4M2	NM_001004719.2	22	0,165,6338	CC,CT,TT		1.2907,1.2256,1.2686	probably-damaging	94/314	22368855	165,12841	2203	4300	6503	SO:0001583	missense	390538	exon1			ATTTCTTTTGATG	AC060768	CCDS32172.1	15q11.2	2013-09-23			ENSG00000182974	ENSG00000182974		"""GPCR / Class A : Olfactory receptors"""	15373	protein-coding gene	gene with protein product							Standard	NM_001004719		Approved		uc010tzu.2	Q8NGB6	OTTHUMG00000171738	ENST00000332663.2:c.280T>C	15.37:g.22368855T>C	ENSP00000329467:p.Phe94Leu	Somatic	266	0	0		WXS	Illumina HiSeq	Phase_I	214	13	0.0607477	NM_001004719	B9EH16|Q6IEY2	Missense_Mutation	SNP	ENST00000332663.2	37	CCDS32172.1	151	0.06913919413919414	16	0.032520325203252036	10	0.027624309392265192	105	0.18356643356643357	20	0.026385224274406333	.	10.46	1.357052	0.24598	0.012256	0.012907	ENSG00000182974	ENST00000332663	T	0.00327	8.09	2.5	2.5	0.30297	GPCR, rhodopsin-like superfamily (1);	0.000000	0.48286	D	0.000188	T	0.00012	0.0000	L	0.55017	1.72	0.09310	N	1	P	0.42409	0.779	B	0.36666	0.23	T	0.47262	-0.9131	10	0.41790	T	0.15	-15.4455	8.5824	0.33637	0.0:0.0:0.0:1.0	.	94	Q8NGB6	OR4M2_HUMAN	L	94	ENSP00000329467:F94L	ENSP00000329467:F94L	F	+	1	0	OR4M2	19870219	0.196000	0.23350	0.925000	0.36789	0.849000	0.48306	3.192000	0.50989	1.167000	0.42706	0.368000	0.22195	TTT	T|0.967;C|0.033	0.033	strong		0.443	OR4M2-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414921.1		
OR4M2	390538	hgsc.bcm.edu	37	15	22369132	22369132	+	Missense_Mutation	SNP	G	G	A	rs112370472	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr15:22369132G>A	ENST00000332663.2	+	1	655	c.557G>A	c.(556-558)cGg>cAg	p.R186Q	RP11-69H14.6_ENST00000558896.1_RNA	NM_001004719.2	NP_001004719.2	Q8NGB6	OR4M2_HUMAN	olfactory receptor, family 4, subfamily M, member 2	186						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(2)|endometrium(2)|kidney(4)|large_intestine(6)|lung(38)|ovary(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)	63		all_cancers(20;1.94e-20)|all_epithelial(15;3.94e-18)|Lung NSC(15;8.53e-15)|all_lung(15;2.87e-14)|Breast(32;0.00519)|Colorectal(260;0.101)	GBM - Glioblastoma multiforme(6;0.124)	all cancers(64;1.64e-11)|Epithelial(43;5.81e-10)|BRCA - Breast invasive adenocarcinoma(123;0.000255)|Kidney(6;0.00736)|KIRC - Kidney renal clear cell carcinoma(6;0.0135)|GBM - Glioblastoma multiforme(186;0.0963)		CAGGTTGTCCGGATTGCCTGT	0.458																																					p.R186Q		Atlas-SNP	.											OR4M2,NS,carcinoma,-1,2	OR4M2	140	2	0			c.G557A						scavenged	.		GLN/ARG	55,4349		0,55,2147	282.0	209.0	234.0		557	2.5	1.0	15	dbSNP_132	234	117,8443		0,117,4163	no	missense	OR4M2	NM_001004719.2	43	0,172,6310	AA,AG,GG		1.3668,1.2489,1.3268	benign	186/314	22369132	172,12792	2202	4280	6482	SO:0001583	missense	390538	exon1			TTGTCCGGATTGC	AC060768	CCDS32172.1	15q11.2	2013-09-23			ENSG00000182974	ENSG00000182974		"""GPCR / Class A : Olfactory receptors"""	15373	protein-coding gene	gene with protein product							Standard	NM_001004719		Approved		uc010tzu.2	Q8NGB6	OTTHUMG00000171738	ENST00000332663.2:c.557G>A	15.37:g.22369132G>A	ENSP00000329467:p.Arg186Gln	Somatic	322	1	0.00310559		WXS	Illumina HiSeq	Phase_I	323	8	0.0247678	NM_001004719	B9EH16|Q6IEY2	Missense_Mutation	SNP	ENST00000332663.2	37	CCDS32172.1	140	0.0641025641025641	18	0.036585365853658534	10	0.027624309392265192	92	0.16083916083916083	20	0.026385224274406333	.	12.37	1.918840	0.33908	0.012489	0.013668	ENSG00000182974	ENST00000332663	T	0.00076	8.76	2.5	2.5	0.30297	GPCR, rhodopsin-like superfamily (1);	0.000000	0.45867	D	0.000336	T	0.00012	0.0000	N	0.17594	0.5	0.25986	N	0.982304	B	0.18310	0.027	B	0.19391	0.025	T	0.38585	-0.9654	10	0.62326	D	0.03	-2.909	5.3487	0.16024	0.1658:0.0:0.8342:0.0	.	186	Q8NGB6	OR4M2_HUMAN	Q	186	ENSP00000329467:R186Q	ENSP00000329467:R186Q	R	+	2	0	OR4M2	19870496	0.000000	0.05858	0.977000	0.42913	0.992000	0.81027	0.388000	0.20735	1.422000	0.47177	0.448000	0.29417	CGG	G|0.973;A|0.027	0.027	strong		0.458	OR4M2-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414921.1		
CHRNA7	1139	hgsc.bcm.edu	37	15	32450704	32450704	+	Silent	SNP	G	G	A	rs201822909		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr15:32450704G>A	ENST00000306901.3	+	7	787	c.690G>A	c.(688-690)acG>acA	p.T230T	CHRNA7_ENST00000455693.2_Silent_p.T49T|CHRNA7_ENST00000454250.3_Silent_p.T259T	NM_000746.5	NP_000737.1	P36544	ACHA7_HUMAN	cholinergic receptor, nicotinic, alpha 7 (neuronal)	230					activation of MAPK activity (GO:0000187)|associative learning (GO:0008306)|B cell activation (GO:0042113)|behavioral response to ethanol (GO:0048149)|behavioral response to nicotine (GO:0035095)|calcium ion transport (GO:0006816)|cation transmembrane transport (GO:0098655)|cellular calcium ion homeostasis (GO:0006874)|cognition (GO:0050890)|dopamine biosynthetic process (GO:0042416)|endocytosis (GO:0006897)|generation of ovulation cycle rhythm (GO:0060112)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|memory (GO:0007613)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 beta production (GO:0032691)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of tumor necrosis factor production (GO:0032720)|neuronal action potential (GO:0019228)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell proliferation (GO:0008284)|positive regulation of heart rate involved in baroreceptor response to decreased systemic arterial blood pressure (GO:0001988)|regulation of norepinephrine secretion (GO:0014061)|regulation of synaptic transmission, dopaminergic (GO:0032225)|response to food (GO:0032094)|response to hypoxia (GO:0001666)|response to nicotine (GO:0035094)|signal transduction (GO:0007165)|sperm motility (GO:0030317)|synaptic transmission (GO:0007268)|synaptic transmission, cholinergic (GO:0007271)|T cell activation (GO:0042110)	acetylcholine-gated channel complex (GO:0005892)|apical plasma membrane (GO:0016324)|asymmetric synapse (GO:0032279)|axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|external side of plasma membrane (GO:0009897)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)	acetylcholine binding (GO:0042166)|acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|acetylcholine-gated cation channel activity (GO:0022848)|beta-amyloid binding (GO:0001540)|chloride channel regulator activity (GO:0017081)|drug binding (GO:0008144)|protein homodimerization activity (GO:0042803)|toxic substance binding (GO:0015643)	p.T230T(1)|p.T140T(1)		endometrium(3)|large_intestine(1)|lung(6)|ovary(2)	12		all_lung(180;6.35e-11)		all cancers(64;3.34e-21)|Epithelial(43;2.64e-15)|GBM - Glioblastoma multiforme(186;5.17e-06)|BRCA - Breast invasive adenocarcinoma(123;0.00112)|Lung(196;0.227)	Amobarbital(DB01351)|Aprobarbital(DB01352)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Dextromethorphan(DB00514)|Galantamine(DB00674)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Methylphenobarbital(DB00849)|Nicotine(DB00184)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Primidone(DB00794)|Secobarbital(DB00418)|Talbutal(DB00306)|Thiopental(DB00599)|Varenicline(DB01273)	GCCGCAGGACGCTCTACTATG	0.582																																					p.T259T	Esophageal Squamous(193;529 2900 40232 43193)	Atlas-SNP	.											CHRNA7_ENST00000437966,caecum,carcinoma,0,11	CHRNA7	57	11	2	Substitution - coding silent(2)	ovary(2)	c.G777A						scavenged	.						119.0	100.0	107.0					15																	32450704		2200	4297	6497	SO:0001819	synonymous_variant	1139	exon7			CAGGACGCTCTAC	Z23141	CCDS10027.1, CCDS53924.1	15q13.3	2012-02-11	2012-02-07		ENSG00000175344	ENSG00000175344		"""Cholinergic receptors"", ""Ligand-gated ion channels / Acetylcholine receptors, nicotinic"""	1960	protein-coding gene	gene with protein product	"""acetylcholine receptor, nicotinic, alpha 7 (neuronal)"""	118511	"""cholinergic receptor, nicotinic, alpha polypeptide 7"""			8188270	Standard	NM_001190455		Approved		uc021sic.2	P36544	OTTHUMG00000129285	ENST00000306901.3:c.690G>A	15.37:g.32450704G>A		Somatic	483	52	0.10766		WXS	Illumina HiSeq	Phase_I	395	56	0.141772	NM_001190455	A8K7Q4|B4DFS0|Q15826|Q8IUZ4|Q96RH2|Q99555|Q9BXH0	Silent	SNP	ENST00000306901.3	37	CCDS10027.1																																																																																			G|0.705;A|0.295	0.295	strong		0.582	CHRNA7-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251410.2		
NEB	4703	hgsc.bcm.edu	37	2	152515683	152515683	+	Splice_Site	SNP	G	G	A	rs75807392	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr2:152515683G>A	ENST00000172853.10	-	47	6118	c.5971C>T	c.(5971-5973)Cat>Tat	p.H1991Y	NEB_ENST00000604864.1_Splice_Site_p.H1991Y|NEB_ENST00000427231.2_Splice_Site_p.H1991Y|NEB_ENST00000603639.1_Splice_Site_p.H1991Y|NEB_ENST00000409198.1_Splice_Site_p.H1991Y|NEB_ENST00000397345.3_Splice_Site_p.H1991Y			P20929	NEBU_HUMAN	nebulin	1991					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)		TTGTAGAGATGCTAGGAAAAA	0.323													G|||	461	0.0920527	0.0083	0.0288	5008	,	,		15218	0.249		0.0696	False		,,,				2504	0.1115				p.H1991Y		Atlas-SNP	.											.	NEB	1697	.	0			c.C5971T						PASS	.	G	TYR/HIS,TYR/HIS,TYR/HIS	58,3602		1,56,1773	177.0	166.0	169.0		5971,5971,5971	4.4	1.0	2	dbSNP_131	169	442,7738		17,408,3665	yes	missense-near-splice,missense-near-splice,missense-near-splice	NEB	NM_001164507.1,NM_001164508.1,NM_004543.4	83,83,83	18,464,5438	AA,AG,GG		5.4034,1.5847,4.223	possibly-damaging,possibly-damaging,possibly-damaging	1991/8526,1991/8526,1991/6670	152515683	500,11340	1830	4090	5920	SO:0001630	splice_region_variant	4703	exon47			AGAGATGCTAGGA	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.5971-1C>T	2.37:g.152515683G>A		Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	190	10	0.0526316	NM_004543	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Missense_Mutation	SNP	ENST00000172853.10	37		221	0.10119047619047619	6	0.012195121951219513	13	0.03591160220994475	148	0.25874125874125875	54	0.0712401055408971	G	1.939	-0.444046	0.04604	0.015847	0.054034	ENSG00000183091	ENST00000409198;ENST00000397345;ENST00000427231;ENST00000172853	T;T;T;T	0.44482	0.92;0.92;0.92;0.92	6.17	4.38	0.52667	.	0.353403	0.32640	N	0.005829	T	0.00012	0.0000	L	0.34521	1.04	0.09310	P	1.0	P	0.39535	0.677	B	0.43701	0.428	T	0.28038	-1.0056	9	0.21014	T	0.42	.	11.2178	0.48835	0.0669:0.0:0.8055:0.1275	.	1991	P20929	NEBU_HUMAN	Y	1991	ENSP00000386259:H1991Y;ENSP00000380505:H1991Y;ENSP00000416578:H1991Y;ENSP00000172853:H1991Y	ENSP00000172853:H1991Y	H	-	1	0	NEB	152223929	1.000000	0.71417	0.998000	0.56505	0.535000	0.34838	1.706000	0.37878	0.931000	0.37242	-0.126000	0.14955	CAT	G|0.913;A|0.087	0.087	strong		0.323	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543	Missense_Mutation
CWF19L1	55280	hgsc.bcm.edu	37	10	102006625	102006625	+	Missense_Mutation	SNP	G	G	A	rs7073610	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr10:102006625G>A	ENST00000354105.4	-	8	862	c.776C>T	c.(775-777)cCg>cTg	p.P259L	CWF19L1_ENST00000478047.1_Intron|CWF19L1_ENST00000370379.1_Missense_Mutation_p.P14L	NM_018294.4	NP_060764.3	Q69YN2	C19L1_HUMAN	CWF19-like 1, cell cycle control (S. pombe)	259			P -> L (in dbSNP:rs7073610).				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)		AGTGACATCCGGAGGCTGTTT	0.428													G|||	401	0.0800719	0.1233	0.0519	5008	,	,		18841	0.0615		0.0487	False		,,,				2504	0.093				p.P259L		Atlas-SNP	.											.	CWF19L1	39	.	0			c.C776T						PASS	.	G	LEU/PRO	420,3986	204.5+/-226.7	23,374,1806	93.0	85.0	87.0		776	4.6	1.0	10	dbSNP_116	87	398,8202	127.2+/-185.5	6,386,3908	yes	missense	CWF19L1	NM_018294.4	98	29,760,5714	AA,AG,GG		4.6279,9.5325,6.2894	benign	259/539	102006625	818,12188	2203	4300	6503	SO:0001583	missense	55280	exon8			ACATCCGGAGGCT	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.776C>T	10.37:g.102006625G>A	ENSP00000326411:p.Pro259Leu	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	149	8	0.0536913	NM_018294	B4DHX1|D3DR66|Q5W0I3|Q96HC3|Q9H865|Q9NV13	Missense_Mutation	SNP	ENST00000354105.4	37	CCDS7489.1	151	0.06913919413919414	49	0.09959349593495935	23	0.06353591160220995	38	0.06643356643356643	41	0.05408970976253298	G	14.05	2.420734	0.42918	0.095325	0.046279	ENSG00000095485	ENST00000354105;ENST00000370379	T;T	0.29397	1.57;1.57	5.56	4.6	0.57074	.	0.102462	0.64402	D	0.000003	T	0.00580	0.0019	L	0.46157	1.445	0.20638	P	0.999874243	B;B	0.22211	0.066;0.05	B;B	0.14023	0.009;0.01	T	0.04607	-1.0939	9	0.25751	T	0.34	-7.4526	6.4374	0.21831	0.0897:0.0:0.7284:0.1818	rs7073610;rs56524184;rs58651039;rs7073610	122;259	Q69YN2-3;Q69YN2	.;C19L1_HUMAN	L	259;14	ENSP00000326411:P259L;ENSP00000359405:P14L	ENSP00000326411:P259L	P	-	2	0	CWF19L1	101996615	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.511000	0.45476	2.634000	0.89283	0.561000	0.74099	CCG	G|0.930;A|0.070	0.070	strong		0.428	CWF19L1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_018294	
MUC21	394263	hgsc.bcm.edu	37	6	30954963	30954963	+	Silent	SNP	G	G	A	rs55956203	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr6:30954963G>A	ENST00000376296.3	+	2	1252	c.1011G>A	c.(1009-1011)acG>acA	p.T337T	MUC21_ENST00000486149.2_5'UTR	NM_001010909.2	NP_001010909.2	Q5SSG8	MUC21_HUMAN	mucin 21, cell surface associated	337	28 X 15 AA approximate tandem repeats.|Ser-rich.				cellular protein metabolic process (GO:0044267)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cell-substrate adhesion (GO:0010812)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.T337T(1)		NS(4)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(4)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	42						AGTCCAGCACGACCTCCAGTG	0.627																																					p.T337T		Atlas-SNP	.											MUC21,NS,carcinoma,0,1	MUC21	98	1	1	Substitution - coding silent(1)	prostate(1)	c.G1011A						scavenged	.						135.0	136.0	136.0					6																	30954963		2203	4296	6499	SO:0001819	synonymous_variant	394263	exon2			CAGCACGACCTCC	AK056612	CCDS34388.1	6p21.33	2008-05-14	2008-05-14	2008-05-14	ENSG00000204544	ENSG00000204544		"""Mucins"""	21661	protein-coding gene	gene with protein product	"""epiglycanin"""		"""chromosome 6 open reading frame 205"""	C6orf205		17977904	Standard	NM_001010909		Approved	bCX31G15.2	uc003nsh.2	Q5SSG8	OTTHUMG00000031216	ENST00000376296.3:c.1011G>A	6.37:g.30954963G>A		Somatic	89	3	0.0337079		WXS	Illumina HiSeq	Phase_I	116	6	0.0517241	NM_001010909	B0UZT7|B4DQ55|C9JMK2|D9N007|Q0VGF1|Q3B7T2|Q5SS94|Q6UXC5	Silent	SNP	ENST00000376296.3	37	CCDS34388.1																																																																																			G|0.932;A|0.068	0.068	strong		0.627	MUC21-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000128579.3	NM_001010909	
KDM3A	55818	hgsc.bcm.edu	37	2	86697367	86697367	+	Silent	SNP	C	C	T	rs189936092	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr2:86697367C>T	ENST00000409556.1	+	12	1925	c.1560C>T	c.(1558-1560)ctC>ctT	p.L520L	KDM3A_ENST00000409064.1_Silent_p.L520L|KDM3A_ENST00000542128.1_Silent_p.L468L|KDM3A_ENST00000485171.1_3'UTR|KDM3A_ENST00000312912.5_Silent_p.L520L			Q9Y4C1	KDM3A_HUMAN	lysine (K)-specific demethylase 3A	520					androgen receptor signaling pathway (GO:0030521)|formaldehyde biosynthetic process (GO:0046293)|histone H3-K9 demethylation (GO:0033169)|histone H3-K9 dimethylation (GO:0036123)|hormone-mediated signaling pathway (GO:0009755)|negative regulation of histone H3-K9 methylation (GO:0051573)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|spermatid nucleus elongation (GO:0007290)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|core promoter binding (GO:0001047)|dioxygenase activity (GO:0051213)|iron ion binding (GO:0005506)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region sequence-specific DNA binding (GO:0000976)	p.L520L(1)		NS(1)|breast(3)|central_nervous_system(2)|endometrium(5)|kidney(5)|large_intestine(7)|liver(1)|lung(13)|ovary(1)|prostate(3)|skin(1)|stomach(3)|upper_aerodigestive_tract(2)	47						CAGCTAAACTCAAAAAGCTGC	0.448													C|||	14	0.00279553	0.0	0.0	5008	,	,		18505	0.0139		0.0	False		,,,				2504	0.0				p.L520L	NSCLC(96;1150 1523 6936 46253 49736)	Atlas-SNP	.											KDM3A,NS,carcinoma,0,2	KDM3A	179	2	1	Substitution - coding silent(1)	stomach(1)	c.C1560T						scavenged	.						97.0	91.0	93.0					2																	86697367		2203	4300	6503	SO:0001819	synonymous_variant	55818	exon11			TAAACTCAAAAAG	AB018285	CCDS1990.1	2p11.2	2011-07-01	2009-04-06	2009-04-06	ENSG00000115548	ENSG00000115548		"""Chromatin-modifying enzymes / K-demethylases"""	20815	protein-coding gene	gene with protein product	"""jumonji C domain-containing histone demethylase 2A"""	611512	"""jumonji domain containing 1"", ""jumonji domain containing 1A"""	JMJD1, JMJD1A		9872452	Standard	NM_018433		Approved	TSGA, KIAA0742, JHMD2A	uc010ytj.2	Q9Y4C1	OTTHUMG00000130204	ENST00000409556.1:c.1560C>T	2.37:g.86697367C>T		Somatic	258	0	0		WXS	Illumina HiSeq	Phase_I	276	6	0.0217391	NM_001146688	D6W5M3|Q53S72|Q68D47|Q68UT9|Q6N050|Q8IY08	Silent	SNP	ENST00000409556.1	37	CCDS1990.1																																																																																			C|0.996;T|0.004	0.004	strong		0.448	KDM3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252522.2	NM_018433	
TWF1	5756	hgsc.bcm.edu	37	12	44196125	44196125	+	Silent	SNP	T	T	C	rs112006889	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr12:44196125T>C	ENST00000395510.2	-	3	375	c.246A>G	c.(244-246)gaA>gaG	p.E82E	TWF1_ENST00000552521.1_5'UTR|TWF1_ENST00000547564.1_5'UTR|TWF1_ENST00000325127.4_Silent_p.E116E|TWF1_ENST00000548315.1_Silent_p.E82E	NM_001242397.1|NM_002822.4	NP_001229326.1|NP_002813.3	Q12792	TWF1_HUMAN	twinfilin actin-binding protein 1	82	ADF-H 1. {ECO:0000255|PROSITE- ProRule:PRU00599}.				barbed-end actin filament capping (GO:0051016)|negative regulation of actin filament polymerization (GO:0030837)|peptidyl-tyrosine phosphorylation (GO:0018108)|regulation of actin phosphorylation (GO:0043538)|sequestering of actin monomers (GO:0042989)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|myofibril (GO:0030016)|perinuclear region of cytoplasm (GO:0048471)|ruffle membrane (GO:0032587)	actin monomer binding (GO:0003785)|ATP binding (GO:0005524)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)			endometrium(2)|large_intestine(6)|lung(4)|prostate(1)|stomach(1)	14	all_cancers(12;0.00125)	Lung NSC(34;0.0804)|all_lung(34;0.181)		GBM - Glioblastoma multiforme(48;0.0474)		TGAATATCCATTCATATCCCT	0.328													T|||	248	0.0495208	0.0393	0.072	5008	,	,		16572	0.0556		0.0119	False		,,,				2504	0.0798				p.E82E		Atlas-SNP	.											TWF1,NS,carcinoma,-2,1	TWF1	37	1	0			c.A246G						scavenged	.	T	,	136,4270	94.8+/-133.5	2,132,2069	51.0	55.0	54.0		246,246	-3.7	1.0	12	dbSNP_132	54	156,8440	73.2+/-135.9	2,152,4144	no	coding-synonymous,coding-synonymous	TWF1	NM_001242397.1,NM_002822.4	,	4,284,6213	CC,CT,TT		1.8148,3.0867,2.2458	,	82/358,82/351	44196125	292,12710	2203	4298	6501	SO:0001819	synonymous_variant	5756	exon3			TATCCATTCATAT	U02680	CCDS31780.1, CCDS31780.2, CCDS55818.1	12q12	2013-04-25	2013-04-25	2006-11-13					9620	protein-coding gene	gene with protein product		610932	"""protein tyrosine kinase 9"", ""PTK9 protein tyrosine kinase 9"", ""twinfilin, actin-binding protein, homolog 1 (Drosophila)"""	PTK9		7507208	Standard	NM_002822		Approved	A6	uc001rob.3	Q12792		ENST00000395510.2:c.246A>G	12.37:g.44196125T>C		Somatic	369	0	0		WXS	Illumina HiSeq	Phase_I	330	8	0.0242424	NM_002822	A8K5A8|B3KXS6|B4DLX9|Q59G07|Q5U0B1|Q6FHJ1|Q6FHL6|Q6NUK9|Q86XL6|Q8TCD3	Silent	SNP	ENST00000395510.2	37	CCDS31780.2																																																																																			T|0.973;C|0.027	0.027	strong		0.328	TWF1-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403956.1	NM_002822	
MUC5B	727897	hgsc.bcm.edu	37	11	1269835	1269835	+	Missense_Mutation	SNP	G	G	A	rs2943521	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr11:1269835G>A	ENST00000529681.1	+	31	11783	c.11725G>A	c.(11725-11727)Gtc>Atc	p.V3909I	MUC5B_ENST00000447027.1_Missense_Mutation_p.V3912I|RP11-532E4.2_ENST00000532061.2_RNA	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	3909	11 X approximate tandem repeats, Ser/Thr- rich.|7 X Cys-rich subdomain repeats.|Thr-rich.			V -> I (in Ref. 4; CAA96577). {ECO:0000305}.	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)		CCCCTCCTCCGTCCCGGGGAC	0.652													A|||	2311	0.461462	0.3185	0.5418	5008	,	,		14910	0.6567		0.4205	False		,,,				2504	0.4387				p.V3909I		Atlas-SNP	.											.	MUC5B	473	.	0			c.G11725A						PASS	.						90.0	102.0	98.0					11																	1269835		2055	4169	6224	SO:0001583	missense	727897	exon31			TCCTCCGTCCCGG	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.11725G>A	11.37:g.1269835G>A	ENSP00000436812:p.Val3909Ile	Somatic	262	0	0		WXS	Illumina HiSeq	Phase_I	337	15	0.0445104	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	37	CCDS44515.2	797	0.3649267399267399	99	0.20121951219512196	132	0.36464088397790057	322	0.5629370629370629	244	0.32189973614775724	A	4.241	0.043603	0.08196	.	.	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637;ENST00000406844	T;T	0.17528	2.27;2.46	3.11	-6.22	0.02058	.	.	.	.	.	T	0.00012	0.0000	N	0.00138	-2.015	0.80722	P	0.0	B;B	0.06786	0.001;0.0	B;B	0.04013	0.001;0.0	T	0.51317	-0.8721	8	0.87932	D	0	.	1.5831	0.02638	0.1585:0.328:0.222:0.2914	rs59902608	4437;3912	A7Y9J9;E9PBJ0	.;.	I	3909;3912;3853;3814	ENSP00000436812:V3909I;ENSP00000415793:V3912I	ENSP00000343037:V3853I	V	+	1	0	MUC5B	1226411	0.000000	0.05858	0.000000	0.03702	0.030000	0.12068	0.108000	0.15396	-4.491000	0.00046	-0.848000	0.03037	GTC	G|0.614;A|0.386	0.386	strong		0.652	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
HS1BP3	64342	hgsc.bcm.edu	37	2	20824559	20824559	+	Silent	SNP	C	C	T	rs2305457	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr2:20824559C>T	ENST00000304031.3	-	5	742	c.717G>A	c.(715-717)gaG>gaA	p.E239E		NM_022460.3	NP_071905.3	Q53T59	H1BP3_HUMAN	HCLS1 binding protein 3	239							phosphatidylinositol binding (GO:0035091)			endometrium(4)|large_intestine(1)|lung(7)|ovary(1)|skin(2)	15	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CAAAGAGCCCCTCATCAGGGT	0.612													C|||	1380	0.275559	0.0333	0.366	5008	,	,		18239	0.4881		0.2614	False		,,,				2504	0.3344				p.E239E		Atlas-SNP	.											.	HS1BP3	33	.	0			c.G717A						PASS	.	C		325,4081	170.1+/-200.6	9,307,1887	74.0	81.0	79.0		717	0.7	0.3	2	dbSNP_100	79	2227,6373	378.2+/-338.8	303,1621,2376	no	coding-synonymous	HS1BP3	NM_022460.3		312,1928,4263	TT,TC,CC		25.8953,7.3763,19.6217		239/393	20824559	2552,10454	2203	4300	6503	SO:0001819	synonymous_variant	64342	exon5			GAGCCCCTCATCA		CCDS1700.1	2p24.1	2006-08-15			ENSG00000118960	ENSG00000118960			24979	protein-coding gene	gene with protein product		609359				10590261, 15699368	Standard	NM_022460		Approved	HS1-BP3,FLJ14249	uc002rdw.1	Q53T59	OTTHUMG00000122099	ENST00000304031.3:c.717G>A	2.37:g.20824559C>T		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	67	6	0.0895522	NM_022460	B2RAW2|D6W529|Q86VC2|Q8N367	Silent	SNP	ENST00000304031.3	37	CCDS1700.1	629	0.288003663003663	21	0.042682926829268296	125	0.3453038674033149	284	0.4965034965034965	199	0.262532981530343	C	0.179	-1.064030	0.01934	0.073763	0.258953	ENSG00000118960	ENST00000445102	.	.	.	4.7	0.696	0.18075	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.58432	P	1.999999999946489E-6	.	.	.	.	.	.	T	0.47661	-0.9100	3	.	.	.	-5.486	3.0218	0.06078	0.172:0.3953:0.3349:0.0978	rs2305457;rs2305457	.	.	.	R	32	.	.	G	-	1	0	HS1BP3	20688040	0.000000	0.05858	0.278000	0.24718	0.003000	0.03518	-0.441000	0.06879	0.580000	0.29522	-0.176000	0.13171	GGG	C|0.772;T|0.228	0.228	strong		0.612	HS1BP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242863.1	NM_022460	
NOTCH2	4853	hgsc.bcm.edu	37	1	120539668	120539668	+	Missense_Mutation	SNP	T	T	A	rs200464440		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr1:120539668T>A	ENST00000256646.2	-	4	922	c.703A>T	c.(703-705)Acc>Tcc	p.T235S	NOTCH2_ENST00000602566.1_Missense_Mutation_p.T196S	NM_024408.3	NP_077719.2	Q04721	NOTC2_HUMAN	notch 2	235	EGF-like 6. {ECO:0000255|PROSITE- ProRule:PRU00076}.				apoptotic process (GO:0006915)|atrial septum morphogenesis (GO:0060413)|bone remodeling (GO:0046849)|cell cycle arrest (GO:0007050)|cell fate determination (GO:0001709)|cell growth (GO:0016049)|ciliary body morphogenesis (GO:0061073)|determination of left/right symmetry (GO:0007368)|embryonic limb morphogenesis (GO:0030326)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|humoral immune response (GO:0006959)|in utero embryonic development (GO:0001701)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|intracellular receptor signaling pathway (GO:0030522)|morphogenesis of an epithelial sheet (GO:0002011)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|placenta blood vessel development (GO:0060674)|positive regulation of apoptotic process (GO:0043065)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cell proliferation (GO:0008284)|positive regulation of Ras protein signal transduction (GO:0046579)|pulmonary valve morphogenesis (GO:0003184)|regulation of transcription, DNA-templated (GO:0006355)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cell surface (GO:0009986)|cilium (GO:0005929)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|ligand-activated RNA polymerase II transcription factor binding transcription factor activity (GO:0038049)|receptor activity (GO:0004872)			breast(4)|central_nervous_system(6)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(9)|kidney(9)|large_intestine(19)|liver(1)|lung(57)|ovary(4)|pancreas(1)|prostate(7)|skin(24)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	158	all_neural(166;0.153)	all_lung(203;1.96e-06)|Lung NSC(69;1.47e-05)|all_epithelial(167;0.000809)		Lung(183;0.0242)|LUSC - Lung squamous cell carcinoma(189;0.133)		TGCCGACAGGTGCCTCCATTG	0.572			"""N, F, Mis"""		"""marginal zone lymphoma, DLBCL"""				Alagille Syndrome																												p.T235S		Atlas-SNP	.		Dom	yes		1	1p13-p11	4853	Notch homolog 2		L	NOTCH2_ENST00000369342,NS,carcinoma,0,2	NOTCH2	348	2	0			c.A703T						scavenged	.						50.0	40.0	43.0					1																	120539668		2203	4299	6502	SO:0001583	missense	4853	exon4	Familial Cancer Database	ALGS1, ALGS2.Alagille-Watson syndrome	GACAGGTGCCTCC	AF315356	CCDS908.1	1p13-p11	2013-01-10	2010-06-24		ENSG00000134250	ENSG00000134250		"""Ankyrin repeat domain containing"""	7882	protein-coding gene	gene with protein product		600275	"""Notch (Drosophila) homolog 2"", ""Notch homolog 2 (Drosophila)"""			7698746	Standard	NM_001200001		Approved		uc001eik.3	Q04721	OTTHUMG00000012177	ENST00000256646.2:c.703A>T	1.37:g.120539668T>A	ENSP00000256646:p.Thr235Ser	Somatic	257	4	0.0155642		WXS	Illumina HiSeq	Phase_I	250	7	0.028	NM_001200001	Q5T3X7|Q99734|Q9H240	Missense_Mutation	SNP	ENST00000256646.2	37	CCDS908.1	.	.	.	.	.	.	.	.	.	.	T	24.2	4.508758	0.85282	.	.	ENSG00000134250	ENST00000256646;ENST00000539617;ENST00000401649;ENST00000369342	T	0.33438	1.41	5.83	5.83	0.93111	Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	0.000000	0.38897	U	0.001527	T	0.42471	0.1204	L	0.58510	1.815	0.80722	D	1	P;D;D	0.71674	0.924;0.998;0.965	P;D;P	0.77004	0.585;0.989;0.834	T	0.25082	-1.0142	10	0.41790	T	0.15	.	15.3661	0.74523	0.0:0.0:0.0:1.0	.	196;235;235	D2WEZ3;Q6IQ50;Q04721	.;.;NOTC2_HUMAN	S	235;196;208;196	ENSP00000256646:T235S	ENSP00000256646:T235S	T	-	1	0	NOTCH2	120341191	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	6.185000	0.72013	2.216000	0.71823	0.477000	0.44152	ACC	.	.	weak		0.572	NOTCH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033679.1	NM_024408	
KLHL5	51088	hgsc.bcm.edu	37	4	39116911	39116911	+	Silent	SNP	T	T	C	rs3733276	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr4:39116911T>C	ENST00000504108.1	+	10	2455	c.2172T>C	c.(2170-2172)acT>acC	p.T724T	KLHL5_ENST00000261426.5_Silent_p.T663T|KLHL5_ENST00000381930.3_Silent_p.T724T|KLHL5_ENST00000359687.2_Silent_p.T724T|RP11-360F5.1_ENST00000509449.1_RNA|KLHL5_ENST00000261425.3_Silent_p.T678T|KLHL5_ENST00000508137.2_Silent_p.T537T	NM_015990.4	NP_057074.3	Q96PQ7	KLHL5_HUMAN	kelch-like family member 5	724						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				endometrium(3)|kidney(1)|large_intestine(11)|lung(9)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	29						ACCTTAATACTGTGGAGGCTT	0.418													C|||	2467	0.492612	0.3411	0.5965	5008	,	,		15980	0.495		0.5765	False		,,,				2504	0.5348				p.T724T		Atlas-SNP	.											.	KLHL5	75	.	0			c.T2172C						PASS	.	C	,,,	1725,2681	651.6+/-399.3	332,1061,810	104.0	94.0	97.0		2034,1611,2172,1989	-3.4	0.9	4	dbSNP_107	97	5039,3561	517.0+/-379.0	1490,2059,751	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	KLHL5	NM_001007075.2,NM_001171654.1,NM_015990.4,NM_199039.3	,,,	1822,3120,1561	CC,CT,TT		41.407,39.1512,47.9932	,,,	678/710,537/569,724/756,663/695	39116911	6764,6242	2203	4300	6503	SO:0001819	synonymous_variant	51088	exon10			TAATACTGTGGAG	AF272976	CCDS3449.1, CCDS33974.1, CCDS33975.1, CCDS54756.1	4p15.1	2013-01-30	2013-01-30		ENSG00000109790	ENSG00000109790		"""Kelch-like"", ""BTB/POZ domain containing"""	6356	protein-coding gene	gene with protein product		608064	"""kelch (Drosophila)-like 5"", ""kelch-like 5 (Drosophila)"""			11590829, 14672410	Standard	NM_001007075		Approved		uc003gtp.3	Q96PQ7	OTTHUMG00000097819	ENST00000504108.1:c.2172T>C	4.37:g.39116911T>C		Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	195	10	0.0512821	NM_015990	A8K170|B7WP68|E9PCF4|F8WAE7|G3XA92|Q6Y881|Q86XW0|Q9NUK3|Q9NV27|Q9NVA9|Q9Y2X2	Silent	SNP	ENST00000504108.1	37	CCDS33974.1	1173	0.5370879120879121	203	0.41260162601626016	227	0.6270718232044199	295	0.5157342657342657	448	0.5910290237467019	C	7.776	0.708499	0.15239	0.391512	0.58593	ENSG00000109790	ENST00000515612	.	.	.	6.06	-3.44	0.04796	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.44967	-0.9293	3	.	.	.	.	0.6333	0.00798	0.2383:0.1979:0.2894:0.2744	rs3733276;rs17430718;rs3733276	.	.	.	R	236	.	.	C	+	1	0	KLHL5	38793306	0.012000	0.17670	0.901000	0.35422	0.859000	0.49053	-0.788000	0.04614	-0.927000	0.03766	-1.068000	0.02270	TGT	T|0.472;C|0.528	0.528	strong		0.418	KLHL5-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000360604.1		
OR13F1	138805	hgsc.bcm.edu	37	9	107266626	107266626	+	Missense_Mutation	SNP	T	T	C	rs79836745	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr9:107266626T>C	ENST00000334726.2	+	1	172	c.83T>C	c.(82-84)tTt>tCt	p.F28S		NM_001004485.1	NP_001004485.1	Q8NGS4	O13F1_HUMAN	olfactory receptor, family 13, subfamily F, member 1	28						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|large_intestine(6)|lung(17)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	31						GTCATCATATTTGCGGTGTGC	0.418													T|||	16	0.00319489	0.0	0.0	5008	,	,		19862	0.0149		0.0	False		,,,				2504	0.001				p.F28S		Atlas-SNP	.											.	OR13F1	75	.	0			c.T83C						PASS	.	T	SER/PHE	0,4406		0,0,2203	132.0	118.0	123.0		83	3.9	0.4	9	dbSNP_132	123	3,8597	3.0+/-9.4	0,3,4297	yes	missense	OR13F1	NM_001004485.1	155	0,3,6500	CC,CT,TT		0.0349,0.0,0.0231	probably-damaging	28/320	107266626	3,13003	2203	4300	6503	SO:0001583	missense	138805	exon1			TCATATTTGCGGT		CCDS35087.1	9q31.1	2013-09-24			ENSG00000186881	ENSG00000186881		"""GPCR / Class A : Olfactory receptors"""	14723	protein-coding gene	gene with protein product							Standard	NM_001004485		Approved		uc011lvm.2	Q8NGS4	OTTHUMG00000020404	ENST00000334726.2:c.83T>C	9.37:g.107266626T>C	ENSP00000334452:p.Phe28Ser	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	124	6	0.0483871	NM_001004485	Q6IF50	Missense_Mutation	SNP	ENST00000334726.2	37	CCDS35087.1	13	0.005952380952380952	0	0.0	0	0.0	13	0.022727272727272728	0	0.0	T	13.67	2.306205	0.40795	0.0	3.49E-4	ENSG00000186881	ENST00000334726	T	0.04551	3.6	3.91	3.91	0.45181	.	0.133830	0.34411	N	0.003984	T	0.09024	0.0223	M	0.72624	2.21	0.43924	D	0.996573	D	0.89917	1.0	D	0.91635	0.999	T	0.00118	-1.2033	10	0.62326	D	0.03	.	11.4142	0.49943	0.0:0.0:0.0:1.0	.	28	Q8NGS4	O13F1_HUMAN	S	28	ENSP00000334452:F28S	ENSP00000334452:F28S	F	+	2	0	OR13F1	106306447	0.995000	0.38212	0.366000	0.25914	0.055000	0.15305	3.535000	0.53575	1.997000	0.58415	0.529000	0.55759	TTT	T|0.991;C|0.009	0.009	strong		0.418	OR13F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053475.1		
ZNF286B	729288	hgsc.bcm.edu	37	17	18565350	18565350	+	Missense_Mutation	SNP	G	G	C	rs9912644	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr17:18565350G>C	ENST00000545289.1	-	5	1719	c.1469C>G	c.(1468-1470)aCc>aGc	p.T490S	ZNF286B_ENST00000285274.5_3'UTR	NM_001145045.1	NP_001138517.1	P0CG31	Z286B_HUMAN	zinc finger protein 286B	490					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)	p.T490S(2)		endometrium(1)|lung(1)	2						TTTCTCTCCGGTATGAGTTCT	0.393													.|||	1496	0.298722	0.2095	0.4092	5008	,	,		22635	0.3611		0.3827	False		,,,				2504	0.1902				p.T490S		Atlas-SNP	.											ZNF286B,NS,carcinoma,0,1	ZNF286B	75	1	2	Substitution - Missense(2)	endometrium(2)	c.C1469G						scavenged	.						103.0	101.0	102.0					17																	18565350		692	1591	2283	SO:0001583	missense	729288	exon5			TCTCCGGTATGAG		CCDS58523.1	17p11.2	2013-01-08			ENSG00000249459	ENSG00000249459		"""Zinc fingers, C2H2-type"""	33241	protein-coding gene	gene with protein product	"""zinc finger protein 590"""		"""zinc finger protein 286-like"", ""zinc finger 286C pseudogene"""	ZNF286L, ZNF286C			Standard	NM_001145045		Approved	ZNF590	uc010vyd.1	P0CG31	OTTHUMG00000178136	ENST00000545289.1:c.1469C>G	17.37:g.18565350G>C	ENSP00000461413:p.Thr490Ser	Somatic	354	0	0		WXS	Illumina HiSeq	Phase_I	317	8	0.0252366	NM_001145045		Missense_Mutation	SNP	ENST00000545289.1	37	CCDS58523.1																																																																																			G|0.648;C|0.352	0.352	strong		0.393	ZNF286B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		XM_001723047	
HEATR5B	54497	hgsc.bcm.edu	37	2	37234302	37234302	+	Silent	SNP	A	A	G	rs74842279	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr2:37234302A>G	ENST00000233099.5	-	29	4763	c.4668T>C	c.(4666-4668)tcT>tcC	p.S1556S	HEATR5B_ENST00000354531.2_Silent_p.S1556S	NM_019024.1	NP_061897.1	Q9P2D3	HTR5B_HUMAN	HEAT repeat containing 5B	1556						extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)		p.S1556S(1)		breast(3)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(11)|lung(31)|ovary(5)|pancreas(1)|prostate(1)|skin(10)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	77		all_hematologic(82;0.21)				TTTGTAAACCAGATATTGCTG	0.433													A|||	26	0.00519169	0.0	0.0	5008	,	,		14841	0.0258		0.0	False		,,,				2504	0.0				p.S1556S		Atlas-SNP	.											HEATR5B,NS,carcinoma,0,1	HEATR5B	185	1	1	Substitution - coding silent(1)	stomach(1)	c.T4668C						scavenged	.						145.0	133.0	137.0					2																	37234302		2203	4300	6503	SO:0001819	synonymous_variant	54497	exon29			TAAACCAGATATT	AB037835	CCDS33181.1	2p22.2	2007-01-02			ENSG00000008869	ENSG00000008869			29273	protein-coding gene	gene with protein product						10718198	Standard	XM_005264379		Approved	KIAA1414, DKFZp686P15184	uc002rpp.1	Q9P2D3	OTTHUMG00000152158	ENST00000233099.5:c.4668T>C	2.37:g.37234302A>G		Somatic	208	0	0		WXS	Illumina HiSeq	Phase_I	217	7	0.0322581	NM_019024	B5MDU8|Q7Z3B2|Q9NVL7	Silent	SNP	ENST00000233099.5	37	CCDS33181.1																																																																																			A|0.988;G|0.012	0.012	strong		0.433	HEATR5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325492.1	NM_019024	
PCDHGA4	56111	hgsc.bcm.edu	37	5	140735617	140735617	+	Missense_Mutation	SNP	G	G	T	rs142728816	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr5:140735617G>T	ENST00000571252.1	+	1	850	c.850G>T	c.(850-852)Gta>Tta	p.V284L	PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA2_ENST00000394576.2_Intron	NM_018917.2	NP_061740	Q9Y5G9	PCDG4_HUMAN	protocadherin gamma subfamily A, 4	284	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(1)|kidney(1)|lung(3)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TTTCCGGAAAGTAAGAGACAA	0.438													.|||	30	0.00599042	0.0	0.0	5008	,	,		21582	0.0278		0.0	False		,,,				2504	0.002				p.V284L		Atlas-SNP	.											.	PCDHGA4	150	.	0			c.G850T						PASS	.						50.0	51.0	51.0					5																	140735617		1913	4125	6038	SO:0001583	missense	56111	exon1			CGGAAAGTAAGAG	AF152511	CCDS58979.1, CCDS58979.2, CCDS75331.1	5q31	2010-01-26						"""Cadherins / Protocadherins : Clustered"""	8702	other	protocadherin		606291				10380929	Standard	NM_018917		Approved	PCDH-GAMMA-A4		Q9Y5G9		ENST00000571252.1:c.850G>T	5.37:g.140735617G>T	ENSP00000458570:p.Val284Leu	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	69	4	0.057971	NM_018917	Q9Y5D3	Missense_Mutation	SNP	ENST00000571252.1	37	CCDS58979.1																																																																																			G|0.994;T|0.006	0.006	strong		0.438	PCDHGA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437959.1	NM_018917	
BANK1	55024	hgsc.bcm.edu	37	4	102816467	102816467	+	Missense_Mutation	SNP	C	C	G	rs62321738	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr4:102816467C>G	ENST00000322953.4	+	6	1183	c.909C>G	c.(907-909)agC>agG	p.S303R	BANK1_ENST00000508653.1_Missense_Mutation_p.S170R|BANK1_ENST00000444316.2_Missense_Mutation_p.S273R|BANK1_ENST00000428908.1_Missense_Mutation_p.S170R|BANK1_ENST00000504592.1_Missense_Mutation_p.S288R	NM_017935.4	NP_060405	Q8NDB2	BANK1_HUMAN	B-cell scaffold protein with ankyrin repeats 1	303	DBB. {ECO:0000255|PROSITE- ProRule:PRU00707}.			S -> R (in Ref. 4; BAF84822). {ECO:0000305}.	B cell activation (GO:0042113)			p.S303R(1)		NS(1)|breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|liver(2)|lung(16)|ovary(2)|skin(2)|urinary_tract(1)	44		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;2.7e-07)		AACAGAATAGCATTGAAGAAC	0.279													C|||	536	0.107029	0.0197	0.2349	5008	,	,		14327	0.1706		0.0805	False		,,,				2504	0.0961				p.S303R		Atlas-SNP	.											BANK1,NS,lymphoid_neoplasm,0,1	BANK1	95	1	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.C909G						scavenged	.	C	ARG/SER,ARG/SER,ARG/SER	153,4253	105.2+/-143.6	1,151,2051	78.0	81.0	80.0		819,510,909	1.8	0.0	4	dbSNP_129	80	538,8054	146.5+/-202.0	20,498,3778	yes	missense,missense,missense	BANK1	NM_001083907.2,NM_001127507.2,NM_017935.4	110,110,110	21,649,5829	GG,GC,CC		6.2616,3.4725,5.3162	benign,benign,benign	273/756,170/653,303/786	102816467	691,12307	2203	4296	6499	SO:0001583	missense	55024	exon6			GAATAGCATTGAA	AB063170	CCDS34038.1, CCDS47115.1, CCDS47116.1	4q23	2013-01-11						"""Ankyrin repeat domain containing"""	18233	protein-coding gene	gene with protein product		610292				11782428, 21208380, 21480188	Standard	NM_017935		Approved	BANK, FLJ20706	uc003hvy.4	Q8NDB2		ENST00000322953.4:c.909C>G	4.37:g.102816467C>G	ENSP00000320509:p.Ser303Arg	Somatic	476	1	0.00210084		WXS	Illumina HiSeq	Phase_I	421	8	0.0190024	NM_017935	A8K7W8|B0F3S2|Q8N5K8|Q8NB56|Q8WYN5|Q9NWP2	Missense_Mutation	SNP	ENST00000322953.4	37	CCDS34038.1	239	0.10943223443223443	13	0.026422764227642278	66	0.18232044198895028	104	0.18181818181818182	56	0.07387862796833773	C	5.883	0.347041	0.11126	0.034725	0.062616	ENSG00000153064	ENST00000504592;ENST00000322953;ENST00000428908;ENST00000508653;ENST00000444316	T;T;T;T;T	0.19806	2.81;2.8;2.12;2.12;2.81	4.94	1.82	0.25136	DBB domain (1);	1.920100	0.02872	N	0.131724	T	0.00073	0.0002	L	0.46157	1.445	0.80722	P	0.0	B;B;B	0.32526	0.018;0.374;0.374	B;B;B	0.38616	0.044;0.186;0.277	T	0.28870	-1.0030	9	0.72032	D	0.01	.	10.2618	0.43431	0.4611:0.5389:0.0:0.0	rs62321738	170;303;288	Q8NDB2-4;Q8NDB2;Q8NDB2-2	.;BANK1_HUMAN;.	R	288;303;170;170;273	ENSP00000421443:S288R;ENSP00000320509:S303R;ENSP00000412748:S170R;ENSP00000422314:S170R;ENSP00000388817:S273R	ENSP00000320509:S303R	S	+	3	2	BANK1	103035490	0.000000	0.05858	0.031000	0.17742	0.398000	0.30690	-0.228000	0.09114	1.017000	0.39495	0.585000	0.79938	AGC	C|0.929;G|0.071	0.071	strong		0.279	BANK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363161.1	NM_017935	
RAB3IL1	5866	hgsc.bcm.edu	37	11	61675610	61675610	+	Silent	SNP	G	G	A			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr11:61675610G>A	ENST00000394836.2	-	2	337	c.180C>T	c.(178-180)gaC>gaT	p.D60D	RAB3IL1_ENST00000301773.5_Silent_p.D107D	NM_013401.2	NP_037533.2	Q8TBN0	R3GEF_HUMAN	RAB3A interacting protein (rabin3)-like 1	60					positive regulation of Rab GTPase activity (GO:0032851)|protein transport (GO:0015031)		Rab guanyl-nucleotide exchange factor activity (GO:0017112)			central_nervous_system(1)|endometrium(2)|large_intestine(2)|liver(1)|lung(4)|skin(3)|urinary_tract(1)	14						GGCGCAACACGTCCAGCTGGG	0.672																																					p.D107D		Atlas-SNP	.											.	RAB3IL1	39	.	0			c.C321T						PASS	.						13.0	14.0	14.0					11																	61675610		2200	4293	6493	SO:0001819	synonymous_variant	5866	exon2			CAACACGTCCAGC	AF084557	CCDS8014.1, CCDS60809.1	11q12.2	2008-02-01			ENSG00000167994	ENSG00000167994			9780	protein-coding gene	gene with protein product							Standard	NM_013401		Approved		uc001nso.4	Q8TBN0	OTTHUMG00000167524	ENST00000394836.2:c.180C>T	11.37:g.61675610G>A		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	46	11	0.23913	NM_001271686	Q86V32|Q9P1Q8	Silent	SNP	ENST00000394836.2	37	CCDS8014.1																																																																																			.	.	none		0.672	RAB3IL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394917.1	NM_013401	
CPS1	1373	hgsc.bcm.edu	37	2	211540507	211540507	+	Missense_Mutation	SNP	C	C	A	rs1047891	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr2:211540507C>A	ENST00000233072.5	+	36	4413	c.4217C>A	c.(4216-4218)aCc>aAc	p.T1406N	CPS1_ENST00000451903.2_Missense_Mutation_p.T955N|CPS1_ENST00000430249.2_Missense_Mutation_p.T1412N	NM_001875.4	NP_001866.2	P31327	CPSM_HUMAN	carbamoyl-phosphate synthase 1, mitochondrial	1406			T -> N (associated with PHN susceptibility; 30-40% higher activity; also highly associated with hepatocellular carcinoma (HCC) progression; dbSNP:rs1047891). {ECO:0000269|PubMed:11407344, ECO:0000269|PubMed:12853138, ECO:0000269|PubMed:12955727, ECO:0000269|PubMed:1840546, ECO:0000269|PubMed:20520828, ECO:0000269|PubMed:21767969, ECO:0000269|PubMed:24237036}.		anion homeostasis (GO:0055081)|carbamoyl phosphate biosynthetic process (GO:0070409)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to cAMP (GO:0071320)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cellular response to glucagon stimulus (GO:0071377)|cellular response to oleic acid (GO:0071400)|citrulline biosynthetic process (GO:0019240)|glutamine catabolic process (GO:0006543)|glycogen catabolic process (GO:0005980)|hepatocyte differentiation (GO:0070365)|homocysteine metabolic process (GO:0050667)|midgut development (GO:0007494)|nitric oxide metabolic process (GO:0046209)|positive regulation of vasodilation (GO:0045909)|response to amine (GO:0014075)|response to amino acid (GO:0043200)|response to dexamethasone (GO:0071548)|response to drug (GO:0042493)|response to food (GO:0032094)|response to growth hormone (GO:0060416)|response to lipopolysaccharide (GO:0032496)|response to starvation (GO:0042594)|response to toxic substance (GO:0009636)|response to zinc ion (GO:0010043)|small molecule metabolic process (GO:0044281)|triglyceride catabolic process (GO:0019433)|urea cycle (GO:0000050)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|carbamoyl-phosphate synthase (ammonia) activity (GO:0004087)|endopeptidase activity (GO:0004175)|glutamate binding (GO:0016595)|modified amino acid binding (GO:0072341)|phospholipid binding (GO:0005543)			breast(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(17)|lung(85)|ovary(8)|pancreas(1)|prostate(6)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	142				Epithelial(149;0.00697)|Lung(261;0.0521)|LUSC - Lung squamous cell carcinoma(261;0.0544)|all cancers(144;0.0843)	Carglumic Acid(DB06775)	GTCCCTGCCACCCCAGTGGCA	0.443													C|||	1445	0.288538	0.3684	0.3429	5008	,	,		16610	0.1389		0.3012	False		,,,				2504	0.2832				p.T1412N		Atlas-SNP	.											.	CPS1	485	.	0			c.C4235A						PASS	.	C	ASN/THR,ASN/THR,ASN/THR	1605,2801	497.2+/-363.8	305,995,903	68.0	68.0	68.0	http://www.ncbi.nlm.nih.gov/pubmed?term	4235,2864,4217	5.2	1.0	2	dbSNP_86	68	2676,5924	428.0+/-355.8	422,1832,2046	yes	missense,missense,missense	CPS1	NM_001122633.2,NM_001122634.2,NM_001875.4	65,65,65	727,2827,2949	AA,AC,CC	http://www.ncbi.nlm.nih.gov/pubmed?term	31.1163,36.4276,32.9156	benign,benign,benign	1412/1507,955/1050,1406/1501	211540507	4281,8725	2203	4300	6503	SO:0001583	missense	1373	exon37			CTGCCACCCCAGT	AF154830	CCDS2393.1, CCDS46505.1, CCDS46506.1	2p	2014-09-17	2010-05-11		ENSG00000021826	ENSG00000021826	6.3.4.16		2323	protein-coding gene	gene with protein product		608307	"""carbamoyl-phosphate synthetase 1, mitochondrial"""				Standard	NM_001122633		Approved		uc002vee.4	P31327	OTTHUMG00000132994	ENST00000233072.5:c.4217C>A	2.37:g.211540507C>A	ENSP00000233072:p.Thr1406Asn	Somatic	215	0	0		WXS	Illumina HiSeq	Phase_I	191	8	0.0418848	NM_001122633	B7Z818|J3KQL0|O43774|Q53TL5|Q59HF8|Q7Z5I5	Missense_Mutation	SNP	ENST00000233072.5	37	CCDS2393.1	586	0.2683150183150183	154	0.3130081300813008	122	0.3370165745856354	81	0.14160839160839161	229	0.3021108179419525	C	14.03	2.413514	0.42817	0.364276	0.311163	ENSG00000021826	ENST00000430249;ENST00000539150;ENST00000233072;ENST00000451903	D;D;D	0.82984	-1.67;-1.67;-1.67	6.08	5.2	0.72013	Methylglyoxal synthase-like domain (4);	0.301714	0.35124	N	0.003423	T	0.00012	0.0000	L	0.48877	1.53	0.37459	P	0.08485100000000001	B;B	0.14012	0.009;0.009	B;B	0.19391	0.025;0.025	T	0.08371	-1.0725	9	0.32370	T	0.25	-11.1012	9.5512	0.39310	0.1496:0.7771:0.0:0.0732	rs1047891;rs2229587;rs3187890;rs7422339;rs52831019;rs7422339	1416;1406	Q59HF8;P31327	.;CPSM_HUMAN	N	1412;1414;1406;955	ENSP00000402608:T1412N;ENSP00000233072:T1406N;ENSP00000406136:T955N	ENSP00000233072:T1406N	T	+	2	0	CPS1	211248752	0.977000	0.34250	1.000000	0.80357	0.981000	0.71138	1.756000	0.38390	1.580000	0.49851	0.591000	0.81541	ACC	C|0.699;A|0.301	0.301	strong		0.443	CPS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256569.5		
MUC4	4585	hgsc.bcm.edu	37	3	195515411	195515411	+	Missense_Mutation	SNP	G	G	T	rs55803325	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr3:195515411G>T	ENST00000463781.3	-	2	3499	c.3040C>A	c.(3040-3042)Cct>Act	p.P1014T	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.P1014T	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													.|||	808	0.161342	0.152	0.1124	5008	,	,		18483	0.2321		0.1352	False		,,,				2504	0.1626				p.P1014T		Atlas-SNP	.											.	MUC4	1505	.	4	Deletion - In frame(4)	stomach(4)	c.C3040A						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>A	3.37:g.195515411G>T	ENSP00000417498:p.Pro1014Thr	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	67	5	0.0746269	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	.	.	.	.	.	.	.	.	.	.	-	4.785	0.145931	0.09134	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.31247	1.51;1.5	0.814	-1.63	0.08345	.	.	.	.	.	T	0.13372	0.0324	N	0.14661	0.345	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.21109	-1.0255	8	.	.	.	.	3.0122	0.06048	0.0:0.2389:0.4536:0.3075	rs55803325	1014	E7ESK3	.	T	1014	ENSP00000417498:P1014T;ENSP00000420243:P1014T	.	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	0.007	strong		0.572	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
MUC5B	727897	hgsc.bcm.edu	37	11	1246941	1246941	+	Missense_Mutation	SNP	A	A	G	rs2672785	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr11:1246941A>G	ENST00000529681.1	+	2	159	c.101A>G	c.(100-102)gAg>gGg	p.E34G	MUC5B_ENST00000447027.1_Missense_Mutation_p.E34G	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	34			E -> G (in dbSNP:rs2672785). {ECO:0000269|PubMed:11713095, ECO:0000269|PubMed:9804771}.		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)		CCGAGCTGGGAGAATGCAGGG	0.642													g|||	1640	0.327476	0.3434	0.2767	5008	,	,		17181	0.4365		0.2406	False		,,,				2504	0.319				p.E34G		Atlas-SNP	.											MUC5B,NS,malignant_melanoma,-1,4	MUC5B	473	4	0			c.A101G						scavenged	.	G	GLY/GLU	1174,2798		178,818,990	26.0	34.0	31.0		101	0.0	0.0	11	dbSNP_100	31	1699,6603		201,1297,2653	yes	missense	MUC5B	NM_002458.2	98	379,2115,3643	GG,GA,AA		20.4649,29.5569,23.4072	benign	34/5763	1246941	2873,9401	1986	4151	6137	SO:0001583	missense	727897	exon2			GCTGGGAGAATGC	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.101A>G	11.37:g.1246941A>G	ENSP00000436812:p.Glu34Gly	Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	248	4	0.016129	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	37	CCDS44515.2	708	0.3241758241758242	177	0.3597560975609756	108	0.2983425414364641	246	0.43006993006993005	177	0.23350923482849603	G	7.391	0.630737	0.14322	0.295569	0.204649	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637	T;T	0.20069	2.1;2.29	3.05	0.0329	0.14177	.	.	.	.	.	T	0.00012	0.0000	N	0.04018	-0.295	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.47328	-0.9126	8	0.87932	D	0	.	0.5156	0.00603	0.2992:0.2414:0.2905:0.1689	rs2672785;rs61649189;rs2672785	34;660;34	Q9HC84;A7Y9J9;E9PBJ0	MUC5B_HUMAN;.;.	G	34	ENSP00000436812:E34G;ENSP00000415793:E34G	ENSP00000343037:E34G	E	+	2	0	MUC5B	1203517	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.925000	0.03992	-0.216000	0.10048	-0.215000	0.12644	GAG	A|0.673;G|0.327	0.327	strong		0.642	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
ZNF100	163227	hgsc.bcm.edu	37	19	21948514	21948514	+	Silent	SNP	C	C	A	rs530281593		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr19:21948514C>A	ENST00000358296.6	-	2	276	c.78G>T	c.(76-78)gtG>gtT	p.V26V	ZNF100_ENST00000596452.1_5'UTR	NM_173531.3	NP_775802.2	Q8IYN0	ZN100_HUMAN	zinc finger protein 100	26					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(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(11)|skin(1)|upper_aerodigestive_tract(1)	21						AATAAGACTGCACCAGAAGAC	0.478													C|||	1	0.000199681	0.0008	0.0	5008	,	,		15991	0.0		0.0	False		,,,				2504	0.0				p.V26V		Atlas-SNP	.											.	ZNF100	62	.	0			c.G78T						PASS	.						91.0	100.0	97.0					19																	21948514		2190	4297	6487	SO:0001819	synonymous_variant	163227	exon2			AGACTGCACCAGA	BC035579	CCDS42538.1	19p13.1	2013-01-08	2003-12-19		ENSG00000197020	ENSG00000197020		"""Zinc fingers, C2H2-type"", ""-"""	12880	protein-coding gene	gene with protein product		603982	"""zinc finger protein 100 (Y1)"""			12477932	Standard	NM_173531		Approved		uc002nqi.3	Q8IYN0		ENST00000358296.6:c.78G>T	19.37:g.21948514C>A		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	73	15	0.205479	NM_173531	Q7M4M0	Silent	SNP	ENST00000358296.6	37	CCDS42538.1																																																																																			.	.	none		0.478	ZNF100-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464087.1	NM_173531	
TTC16	158248	hgsc.bcm.edu	37	9	130480025	130480025	+	Missense_Mutation	SNP	C	C	T	rs117963786	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr9:130480025C>T	ENST00000373289.3	+	4	480	c.400C>T	c.(400-402)Cgc>Tgc	p.R134C	TTC16_ENST00000393748.4_5'UTR|PTRH1_ENST00000419060.1_Intron|PTRH1_ENST00000423807.1_5'Flank|PTRH1_ENST00000543175.1_5'Flank|PTRH1_ENST00000429848.1_Intron	NM_144965.1	NP_659402.1	Q8NEE8	TTC16_HUMAN	tetratricopeptide repeat domain 16	134										central_nervous_system(2)|endometrium(3)|lung(7)|ovary(3)|pancreas(2)|prostate(4)|skin(1)	22						GCACCTGGAGCGCCTCACCTT	0.647													C|||	42	0.00838658	0.003	0.0	5008	,	,		15784	0.0367		0.0	False		,,,				2504	0.001				p.R134C		Atlas-SNP	.											.	TTC16	55	.	0			c.C400T						PASS	.	C	CYS/ARG	11,4395	17.9+/-39.9	0,11,2192	58.0	59.0	59.0		400	4.6	0.5	9	dbSNP_132	59	4,8596	3.7+/-12.6	0,4,4296	yes	missense	TTC16	NM_144965.1	180	0,15,6488	TT,TC,CC		0.0465,0.2497,0.1153	probably-damaging	134/874	130480025	15,12991	2203	4300	6503	SO:0001583	missense	158248	exon4			CTGGAGCGCCTCA	AK057342	CCDS6875.1	9q34.13	2013-01-10			ENSG00000167094	ENSG00000167094		"""Tetratricopeptide (TTC) repeat domain containing"""	26536	protein-coding gene	gene with protein product						12477932	Standard	NM_144965		Approved	FLJ32780	uc004brq.1	Q8NEE8	OTTHUMG00000020711	ENST00000373289.3:c.400C>T	9.37:g.130480025C>T	ENSP00000362386:p.Arg134Cys	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	62	5	0.0806452	NM_144965	B4DYG4|B5ME24|Q5JU66|Q96M72	Missense_Mutation	SNP	ENST00000373289.3	37	CCDS6875.1	22	0.010073260073260074	2	0.0040650406504065045	0	0.0	20	0.03496503496503497	0	0.0	C	13.51	2.258983	0.39896	0.002497	4.65E-4	ENSG00000167094	ENST00000373289	T	0.54866	0.55	4.6	4.6	0.57074	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.093873	0.42294	D	0.000734	T	0.45196	0.1330	M	0.78637	2.42	0.37317	D	0.909407	D;D	0.89917	1.0;1.0	D;D	0.68621	0.959;0.959	T	0.69098	-0.5235	10	0.87932	D	0	-42.5384	8.7037	0.34340	0.0:0.8944:0.0:0.1056	.	121;134	B4DZ42;Q8NEE8	.;TTC16_HUMAN	C	134	ENSP00000362386:R134C	ENSP00000362386:R134C	R	+	1	0	TTC16	129519846	0.991000	0.36638	0.456000	0.27044	0.136000	0.21042	3.149000	0.50655	2.132000	0.65825	0.313000	0.20887	CGC	C|0.996;T|0.004	0.004	strong		0.647	TTC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054224.1	NM_144965	
SYT8	90019	hgsc.bcm.edu	37	11	1858262	1858262	+	Missense_Mutation	SNP	C	C	T	rs484955	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr11:1858262C>T	ENST00000381968.3	+	8	1036	c.908C>T	c.(907-909)aCg>aTg	p.T303M	TNNI2_ENST00000381906.1_5'Flank|SYT8_ENST00000341958.3_Missense_Mutation_p.T289M|SYT8_ENST00000535046.1_3'UTR|TNNI2_ENST00000381911.1_5'Flank|TNNI2_ENST00000252898.7_5'Flank	NM_138567.3	NP_612634	Q8NBV8	SYT8_HUMAN	synaptotagmin VIII	303	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				acrosome reaction (GO:0007340)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	transporter activity (GO:0005215)			breast(1)|large_intestine(1)|lung(2)|ovary(1)|skin(1)	6		all_epithelial(84;0.000138)|Breast(177;0.000962)|Ovarian(85;0.0014)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00136)|Lung(200;0.0681)|LUSC - Lung squamous cell carcinoma(625;0.082)		AAAAAGGGCACGGCGGCCCCC	0.622													C|||	929	0.185503	0.0507	0.2262	5008	,	,		18566	0.4137		0.1282	False		,,,				2504	0.1626				p.T303M		Atlas-SNP	.											SYT8,colon,carcinoma,0,1	SYT8	29	1	0			c.C908T						PASS	.	C	MET/THR	270,4134	151.0+/-185.0	12,246,1944	97.0	112.0	107.0		908	2.3	0.1	11	dbSNP_83	107	1035,7563	219.7+/-257.6	60,915,3324	yes	missense	SYT8	NM_138567.3	81	72,1161,5268	TT,TC,CC		12.0377,6.1308,10.0369	probably-damaging	303/402	1858262	1305,11697	2202	4299	6501	SO:0001583	missense	90019	exon8			AGGGCACGGCGGC	AL137708	CCDS7726.2	11p15.5	2013-01-21			ENSG00000149043	ENSG00000149043		"""Synaptotagmins"""	19264	protein-coding gene	gene with protein product		607719				7791877	Standard	XM_005253216		Approved	DKFZp434K0322	uc001lue.1	Q8NBV8	OTTHUMG00000009026	ENST00000381968.3:c.908C>T	11.37:g.1858262C>T	ENSP00000371394:p.Thr303Met	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	125	6	0.048	NM_138567	A6NFJ4|Q9NSV9	Missense_Mutation	SNP	ENST00000381968.3	37	CCDS7726.2	417	0.19093406593406592	22	0.044715447154471545	80	0.22099447513812154	220	0.38461538461538464	95	0.12532981530343007	c	13.83	2.354034	0.41700	0.061308	0.120377	ENSG00000149043	ENST00000381968;ENST00000341958	T;T	0.12039	2.72;2.72	3.28	2.34	0.29019	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	.	.	.	.	T	0.00012	0.0000	H	0.94620	3.56	0.09310	P	1.0	D;D	0.89917	1.0;1.0	D;D	0.79784	0.993;0.993	T	0.29274	-1.0017	8	0.87932	D	0	.	10.6724	0.45766	0.0:0.9005:0.0:0.0995	rs484955;rs484955	303;289	Q8NBV8;A6NCR4	SYT8_HUMAN;.	M	303;289	ENSP00000371394:T303M;ENSP00000343691:T289M	ENSP00000343691:T289M	T	+	2	0	SYT8	1814838	0.689000	0.27690	0.051000	0.19133	0.176000	0.22953	2.807000	0.47955	0.720000	0.32209	0.436000	0.28706	ACG	C|0.863;T|0.137	0.137	strong		0.622	SYT8-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000025013.4		
ALPK3	57538	hgsc.bcm.edu	37	15	85401419	85401419	+	Silent	SNP	T	T	C	rs167379	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr15:85401419T>C	ENST00000258888.5	+	6	4223	c.4056T>C	c.(4054-4056)ggT>ggC	p.G1352G		NM_020778.4	NP_065829.3	Q96L96	ALPK3_HUMAN	alpha-kinase 3	1352					heart development (GO:0007507)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(3)|breast(2)|central_nervous_system(2)|endometrium(12)|kidney(4)|large_intestine(9)|lung(27)|ovary(3)|prostate(5)|skin(8)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	81			BRCA - Breast invasive adenocarcinoma(143;0.0587)			CTCTGACAGGTCTCCCGGCAG	0.647													t|||	4246	0.847843	0.8729	0.7637	5008	,	,		16006	0.9554		0.8131	False		,,,				2504	0.7986				p.G1352G		Atlas-SNP	.											ALPK3_ENST00000258888,NS,carcinoma,0,2	ALPK3	289	2	0			c.T4056C						scavenged	.			3822,582		1655,512,35	16.0	21.0	19.0		4056	-11.2	0.0	15	dbSNP_79	19	7070,1528		2911,1248,140	yes	coding-synonymous	ALPK3	NM_020778.4		4566,1760,175	CC,CT,TT		17.7716,13.2153,16.2283		1352/1908	85401419	10892,2110	2202	4299	6501	SO:0001819	synonymous_variant	57538	exon6			GACAGGTCTCCCG	AY044449	CCDS10333.1	15q25.2	2013-01-29			ENSG00000136383	ENSG00000136383		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	17574	protein-coding gene	gene with protein product	"""myocyte induction differentiation originator"", ""muscle alpha-kinase"""					10021370	Standard	NM_020778		Approved	MAK, KIAA1330, Midori	uc002ble.3	Q96L96	OTTHUMG00000148667	ENST00000258888.5:c.4056T>C	15.37:g.85401419T>C		Somatic	113	1	0.00884956		WXS	Illumina HiSeq	Phase_I	157	3	0.0191083	NM_020778	Q9P2L6	Silent	SNP	ENST00000258888.5	37	CCDS10333.1																																																																																			T|0.150;C|0.850	0.850	strong		0.647	ALPK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308997.1	NM_020778	
TNXB	7148	hgsc.bcm.edu	37	6	32032743	32032743	+	Silent	SNP	G	G	A	rs204883	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr6:32032743G>A	ENST00000375244.3	-	19	6897	c.6696C>T	c.(6694-6696)gaC>gaT	p.D2232D	TNXB_ENST00000375247.2_Silent_p.D2232D			P22105	TENX_HUMAN	tenascin XB	2304	Fibronectin type-III 14. {ECO:0000255|PROSITE-ProRule:PRU00316}.				actin cytoskeleton organization (GO:0030036)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|collagen fibril organization (GO:0030199)|collagen metabolic process (GO:0032963)|elastic fiber assembly (GO:0048251)|extracellular fibril organization (GO:0043206)|fatty acid metabolic process (GO:0006631)|regulation of JUN kinase activity (GO:0043506)|single organismal cell-cell adhesion (GO:0016337)|triglyceride metabolic process (GO:0006641)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|integrin binding (GO:0005178)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)	8						TGGGCTGCCCGTCCCCATTCT	0.597													G|||	1997	0.398762	0.2224	0.4697	5008	,	,		17666	0.4772		0.4463	False		,,,				2504	0.4571				p.D2232D		Atlas-SNP	.											.	TNXB	553	.	0			c.C6696T						PASS	.	G		670,1838		91,488,675	30.0	34.0	33.0		6696	-6.9	0.2	6	dbSNP_79	33	2050,3030		431,1188,921	no	coding-synonymous	TNXB	NM_019105.6		522,1676,1596	AA,AG,GG		40.3543,26.7145,35.8461		2232/4243	32032743	2720,4868	1254	2540	3794	SO:0001819	synonymous_variant	7148	exon19			CTGCCCGTCCCCA	X71923	CCDS4736.1	6p21.3	2013-02-11			ENSG00000168477	ENSG00000168477		"""Fibrinogen C domain containing"", ""Fibronectin type III domain containing"""	11976	protein-coding gene	gene with protein product		600985		TNXB1, TNXB2		8530023	Standard	NM_019105		Approved	TNXBS, XBS, XB	uc021yvf.2	P22105	OTTHUMG00000031088	ENST00000375244.3:c.6696C>T	6.37:g.32032743G>A		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	96	6	0.0625	NM_019105	P78530|P78531|Q08424|Q08AM0|Q08AM1|Q59GU7|Q5SQD3|Q5ST74|Q7L8Q4|Q8N4R1|Q9NPK9|Q9UC10|Q9UC11|Q9UC12|Q9UC13|Q9UMG7	Silent	SNP	ENST00000375244.3	37																																																																																				G|0.569;A|0.431	0.431	strong		0.597	TNXB-001	PUTATIVE	not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000268927.2	NM_019105	
N4BP2	55728	hgsc.bcm.edu	37	4	40138676	40138676	+	Missense_Mutation	SNP	A	A	G	rs2271395	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr4:40138676A>G	ENST00000261435.6	+	14	5175	c.4759A>G	c.(4759-4761)Act>Gct	p.T1587A		NM_018177.4	NP_060647.2	Q86UW6	N4BP2_HUMAN	NEDD4 binding protein 2	1587			T -> A (in dbSNP:rs2271395).		nucleic acid phosphodiester bond hydrolysis (GO:0090305)|phosphorylation (GO:0016310)	cytosol (GO:0005829)	ATP binding (GO:0005524)|ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity (GO:0046404)|endonuclease activity (GO:0004519)			breast(4)|endometrium(3)|kidney(12)|large_intestine(7)|liver(2)|lung(22)|ovary(1)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)	60						CACATCTCATACTGGCCAGAA	0.343													A|||	644	0.128594	0.0076	0.0403	5008	,	,		16869	0.3998		0.0517	False		,,,				2504	0.1544				p.T1587A		Atlas-SNP	.											.	N4BP2	166	.	0			c.A4759G						PASS	.	A	ALA/THR	85,4321	73.6+/-111.7	0,85,2118	73.0	72.0	72.0		4759	2.9	1.0	4	dbSNP_100	72	395,8205	127.2+/-185.5	14,367,3919	yes	missense	N4BP2	NM_018177.4	58	14,452,6037	GG,GA,AA		4.593,1.9292,3.6906	benign	1587/1771	40138676	480,12526	2203	4300	6503	SO:0001583	missense	55728	exon14			TCTCATACTGGCC	AB037834	CCDS3457.1	4p14	2008-01-18			ENSG00000078177	ENSG00000078177			29851	protein-coding gene	gene with protein product	"""BCL-3 binding protein"""					10718198, 11717310	Standard	NM_018177		Approved	B3BP	uc003guy.4	Q86UW6	OTTHUMG00000128599	ENST00000261435.6:c.4759A>G	4.37:g.40138676A>G	ENSP00000261435:p.Thr1587Ala	Somatic	419	0	0		WXS	Illumina HiSeq	Phase_I	470	19	0.0404255	NM_018177	A0AVR3|Q9NVK2|Q9P2D4	Missense_Mutation	SNP	ENST00000261435.6	37	CCDS3457.1	317|317	0.14514652014652016|0.14514652014652016	5|5	0.01016260162601626|0.01016260162601626	16|16	0.04419889502762431|0.04419889502762431	260|260	0.45454545454545453|0.45454545454545453	36|36	0.047493403693931395|0.047493403693931395	A|A	9.740|9.740	1.164654|1.164654	0.21538|0.21538	0.019292|0.019292	0.04593|0.04593	ENSG00000078177|ENSG00000078177	ENST00000261435;ENST00000381804|ENST00000513269	T|.	0.17691|.	2.26|.	5.41|5.41	2.91|2.91	0.33838|0.33838	.|.	0.397696|.	0.24141|.	N|.	0.041178|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.19112|0.19112	0.55|0.55	0.44927|0.44927	P|P	0.002055000000000029|0.002055000000000029	B;B|.	0.33171|.	0.4;0.278|.	B;B|.	0.33960|.	0.173;0.084|.	T|T	0.48536|0.48536	-0.9027|-0.9027	9|4	0.33940|.	T|.	0.23|.	-12.4649|-12.4649	5.2482|5.2482	0.15508|0.15508	0.6522:0.0:0.0747:0.2731|0.6522:0.0:0.0747:0.2731	rs2271395;rs52816843;rs2271395|rs2271395;rs52816843;rs2271395	1587;1587|.	Q86UW6-2;Q86UW6|.	.;N4BP2_HUMAN|.	A|C	1587;1507|1233	ENSP00000261435:T1587A|.	ENSP00000261435:T1587A|.	T|Y	+|+	1|2	0|0	N4BP2|N4BP2	39815071|39815071	0.313000|0.313000	0.24554|0.24554	0.994000|0.994000	0.49952|0.49952	0.462000|0.462000	0.32619|0.32619	1.060000|1.060000	0.30530|0.30530	0.329000|0.329000	0.23460|0.23460	0.460000|0.460000	0.39030|0.39030	ACT|TAC	A|0.918;G|0.082	0.082	strong		0.343	N4BP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250458.2	NM_018177	
NUDT6	11162	hgsc.bcm.edu	37	4	123814308	123814308	+	Missense_Mutation	SNP	C	C	T	rs1048201	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr4:123814308C>T	ENST00000304430.5	-	5	659	c.626G>A	c.(625-627)cGg>cAg	p.R209Q	NUDT6_ENST00000339154.2_Missense_Mutation_p.R40Q|FGF2_ENST00000264498.3_3'UTR|NUDT6_ENST00000608639.1_5'Flank|NUDT6_ENST00000502270.1_Missense_Mutation_p.R40Q|FGF2_ENST00000608478.1_3'UTR	NM_007083.4	NP_009014.2	P53370	NUDT6_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 6	209	Nudix hydrolase. {ECO:0000255|PROSITE- ProRule:PRU00794}.		R -> Q (in dbSNP:rs1048201).			mitochondrion (GO:0005739)|nucleus (GO:0005634)	growth factor activity (GO:0008083)|hydrolase activity (GO:0016787)	p.R40Q(2)|p.R209Q(1)		endometrium(2)|lung(1)|prostate(1)|skin(1)|stomach(1)	6						GTGCTGTTGCCGAATACTCAG	0.403													C|||	1146	0.228834	0.0416	0.1499	5008	,	,		18285	0.4554		0.1779	False		,,,				2504	0.3569				p.R209Q		Atlas-SNP	.											NUDT6_ENST00000304430,NS,carcinoma,0,3	NUDT6	50	3	3	Substitution - Missense(3)	prostate(2)|stomach(1)	c.G626A	GRCh37	CM065349	NUDT6	M	rs1048201	PASS	.	C	,GLN/ARG,GLN/ARG	289,4117	158.9+/-191.5	10,269,1924	87.0	91.0	90.0		,626,119	5.4	1.0	4	dbSNP_86	90	1501,7099	284.4+/-296.6	136,1229,2935	yes	utr-3,missense,missense	FGF2,NUDT6	NM_002006.4,NM_007083.3,NM_198041.1	,43,43	146,1498,4859	TT,TC,CC		17.4535,6.5592,13.7629	,probably-damaging,probably-damaging	,209/317,40/148	123814308	1790,11216	2203	4300	6503	SO:0001583	missense	11162	exon5			TGTTGCCGAATAC	AF019632	CCDS3729.1, CCDS43268.1	4q26	2011-02-21			ENSG00000170917	ENSG00000170917		"""Nudix motif containing"""	8053	protein-coding gene	gene with protein product		606261				7984147, 10022609	Standard	NM_198041		Approved	gfg-1, gfg, FGF2AS, FGF-AS	uc003iew.3	P53370	OTTHUMG00000039507	ENST00000304430.5:c.626G>A	4.37:g.123814308C>T	ENSP00000306070:p.Arg209Gln	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	77	5	0.0649351	NM_007083	A8K756|O95097|Q9UQD9	Missense_Mutation	SNP	ENST00000304430.5	37	CCDS43268.1	472	0.21611721611721613	18	0.036585365853658534	56	0.15469613259668508	262	0.458041958041958	136	0.17941952506596306	C	33	5.258099	0.95368	0.065592	0.174535	ENSG00000170917	ENST00000304430;ENST00000339154;ENST00000502270	T;T;T	0.07688	3.17;3.17;3.17	5.41	5.41	0.78517	NUDIX hydrolase domain (3);NUDIX hydrolase domain-like (1);	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	M	0.89840	3.065	0.09310	P	0.99999999579817	D	0.89917	1.0	D	0.91635	0.999	T	0.41233	-0.9520	9	0.66056	D	0.02	-11.2049	19.2326	0.93846	0.0:1.0:0.0:0.0	rs1048201;rs3172523;rs3804157;rs52813414;rs58707045;rs1048201	209	P53370	NUDT6_HUMAN	Q	209;40;40	ENSP00000306070:R209Q;ENSP00000344011:R40Q;ENSP00000424117:R40Q	ENSP00000306070:R209Q	R	-	2	0	NUDT6	124033758	1.000000	0.71417	0.998000	0.56505	0.948000	0.59901	7.013000	0.76373	2.538000	0.85594	0.650000	0.86243	CGG	C|0.825;T|0.175	0.175	strong		0.403	NUDT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095331.3	NM_007083	
ZNF493	284443	hgsc.bcm.edu	37	19	21606429	21606429	+	Missense_Mutation	SNP	G	G	T	rs4621113	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr19:21606429G>T	ENST00000355504.4	+	2	850	c.584G>T	c.(583-585)tGt>tTt	p.C195F	CTD-2561J22.3_ENST00000600810.1_Intron|ZNF493_ENST00000392288.2_Missense_Mutation_p.C323F	NM_175910.6	NP_787106.4	Q6ZR52	ZN493_HUMAN	zinc finger protein 493	195			C -> F (in dbSNP:rs4621113). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:17974005, ECO:0000269|Ref.2}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	30						CCCTATAAATGTGAAGAATGT	0.333													.|||	2943	0.58766	0.6589	0.5476	5008	,	,		19736	0.6319		0.5	False		,,,				2504	0.5644				p.C323F		Atlas-SNP	.											.	ZNF493	178	.	0			c.G968T						PASS	.	G	PHE/CYS,PHE/CYS	2757,1641		867,1023,309	32.0	37.0	35.0		968,584	1.0	0.2	19	dbSNP_111	35	4437,4151		1205,2027,1062	no	missense,missense	ZNF493	NM_001076678.2,NM_175910.6	205,205	2072,3050,1371	TT,TG,GG		48.3349,37.3124,44.6019	probably-damaging,probably-damaging	323/775,195/647	21606429	7194,5792	2199	4294	6493	SO:0001583	missense	284443	exon4			ATAAATGTGAAGA	AK093823, BC006408, BC022394	CCDS12412.1, CCDS42536.1, CCDS12411.1	19p12	2013-01-08			ENSG00000196268	ENSG00000196268		"""Zinc fingers, C2H2-type"", ""-"""	23708	protein-coding gene	gene with protein product							Standard	NM_001076678		Approved	FLJ36504	uc002npw.3	Q6ZR52	OTTHUMG00000141297	ENST00000355504.4:c.584G>T	19.37:g.21606429G>T	ENSP00000347691:p.Cys195Phe	Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	123	5	0.0406504	NM_001076678	G5E974|Q59GM3|Q6ZSF6|Q8N1Z6|Q8N965|Q9BR99	Missense_Mutation	SNP	ENST00000355504.4	37	CCDS12412.1	1284	0.5879120879120879	334	0.6788617886178862	202	0.5580110497237569	378	0.6608391608391608	370	0.48812664907651715	N	5.820	0.335504	0.11013	0.626876	0.516651	ENSG00000196268	ENST00000392288;ENST00000355504	D;D	0.85088	-1.94;-1.94	0.985	0.985	0.19779	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	M	0.94101	3.495	0.09310	P	1.0	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.46992	-0.9151	8	0.87932	D	0	.	8.7583	0.34658	0.0:0.0:1.0:0.0	rs4621113;rs4621113	195;323	Q6ZR52;Q6ZR52-2	ZN493_HUMAN;.	F	323;195	ENSP00000376110:C323F;ENSP00000347691:C195F	ENSP00000347691:C195F	C	+	2	0	ZNF493	21398269	1.000000	0.71417	0.194000	0.23346	0.190000	0.23558	6.598000	0.74122	0.399000	0.25367	0.404000	0.27445	TGT	G|0.458;T|0.542	0.542	strong		0.333	ZNF493-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000280563.1	NM_175910	
FSCB	84075	hgsc.bcm.edu	37	14	44975052	44975052	+	Missense_Mutation	SNP	A	A	G	rs3825630	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr14:44975052A>G	ENST00000340446.4	-	1	1430	c.1139T>C	c.(1138-1140)cTt>cCt	p.L380P	RP11-163M18.1_ENST00000557465.1_RNA|RP11-163M18.1_ENST00000555433.1_RNA	NM_032135.3	NP_115511.3	Q5H9T9	FSCB_HUMAN	fibrous sheath CABYR binding protein	380	Pro-rich.		L -> P (in dbSNP:rs3825630). {ECO:0000269|PubMed:15489334}.			sperm fibrous sheath (GO:0035686)|sperm principal piece (GO:0097228)	calcium ion binding (GO:0005509)	p.L380P(1)		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)		TTCACCAAGAAGCTCTACTGA	0.522													A|||	1358	0.271166	0.2859	0.3055	5008	,	,		18322	0.3968		0.1193	False		,,,				2504	0.2536				p.L380P		Atlas-SNP	.											FSCB,NS,carcinoma,0,1	FSCB	173	1	1	Substitution - Missense(1)	stomach(1)	c.T1139C						PASS	.	A	PRO/LEU	1168,3238	363.6+/-316.6	160,848,1195	88.0	101.0	97.0		1139	-0.2	0.0	14	dbSNP_107	97	938,7662	196.9+/-241.7	50,838,3412	yes	missense	FSCB	NM_032135.3	98	210,1686,4607	GG,GA,AA		10.907,26.5093,16.1925	probably-damaging	380/826	44975052	2106,10900	2203	4300	6503	SO:0001583	missense	84075	exon1			CCAAGAAGCTCTA	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.1139T>C	14.37:g.44975052A>G	ENSP00000344579:p.Leu380Pro	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	133	7	0.0526316	NM_032135	Q5H9U7|Q86YI2|Q9H0J3	Missense_Mutation	SNP	ENST00000340446.4	37	CCDS9679.1	542	0.24816849816849818	138	0.2804878048780488	97	0.26795580110497236	223	0.38986013986013984	84	0.11081794195250659	a	4.879	0.163307	0.09287	0.265093	0.10907	ENSG00000189139	ENST00000340446;ENST00000537803	T	0.17528	2.27	3.87	-0.16	0.13375	.	.	.	.	.	T	0.00012	0.0000	N	0.17474	0.49	0.80722	P	0.0	B	0.11235	0.004	B	0.08055	0.003	T	0.48502	-0.9030	8	0.30078	T	0.28	.	6.2119	0.20633	0.5846:0.0:0.4154:0.0	rs3825630;rs17855636;rs58475266;rs3825630	380	Q5H9T9	FSCB_HUMAN	P	380	ENSP00000344579:L380P	ENSP00000344579:L380P	L	-	2	0	FSCB	44044802	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-0.903000	0.04084	-0.139000	0.11414	-0.479000	0.04858	CTT	A|0.796;G|0.204	0.204	strong		0.522	FSCB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276788.1	NM_032135	
MISP	126353	hgsc.bcm.edu	37	19	757399	757399	+	Silent	SNP	A	A	C	rs3746172	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr19:757399A>C	ENST00000215582.6	+	2	556	c.453A>C	c.(451-453)gcA>gcC	p.A151A		NM_173481.2	NP_775752.1	Q8IVT2	MISP_HUMAN	mitotic spindle positioning	151					mitotic nuclear division (GO:0007067)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)											AGGGCCAGGCAGTCAGGAAGA	0.687													A|||	1219	0.243411	0.3601	0.2277	5008	,	,		16778	0.3542		0.1004	False		,,,				2504	0.1299				p.A151A		Atlas-SNP	.											C19orf21,NS,carcinoma,+2,1	C19orf21	56	1	0			c.A453C						PASS	.	A		1278,3112		179,920,1096	33.0	33.0	33.0		453	-7.2	0.0	19	dbSNP_107	33	831,7759		39,753,3503	no	coding-synonymous	C19orf21	NM_173481.2		218,1673,4599	CC,CA,AA		9.674,29.1116,16.2481		151/680	757399	2109,10871	2195	4295	6490	SO:0001819	synonymous_variant	126353	exon2			CCAGGCAGTCAGG	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.453A>C	19.37:g.757399A>C		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	96	5	0.0520833	NM_173481		Silent	SNP	ENST00000215582.6	37	CCDS12042.1																																																																																			A|0.819;C|0.181	0.181	strong		0.687	MISP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457600.2	NM_173481	
IKBIP	121457	hgsc.bcm.edu	37	12	99007623	99007623	+	Missense_Mutation	SNP	C	C	T	rs1048906	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr12:99007623C>T	ENST00000342502.2	-	3	1204	c.793G>A	c.(793-795)Ggt>Agt	p.G265S	IKBIP_ENST00000393042.3_3'UTR|IKBIP_ENST00000420861.1_Missense_Mutation_p.G159S	NM_201612.2	NP_963906.1	Q70UQ0	IKIP_HUMAN	IKBKB interacting protein	265			G -> S (in dbSNP:rs1048906).		response to X-ray (GO:0010165)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				NS(1)|kidney(1)|large_intestine(1)|lung(1)|prostate(2)	6						GCTCTGTCACCTTCTAAGCTT	0.358													T|||	1956	0.390575	0.5295	0.3329	5008	,	,		19240	0.3492		0.2982	False		,,,				2504	0.3814				p.G265S		Atlas-SNP	.											.	IKBIP	46	.	0			c.G793A						PASS	.	T	SER/GLY,	2199,2205	588.1+/-386.8	566,1067,569	127.0	131.0	129.0		793,	1.9	1.0	12	dbSNP_86	129	2699,5899	681.8+/-403.7	424,1851,2024	yes	missense,utr-3	IKBIP	NM_201612.1,NM_201613.1	56,	990,2918,2593	TT,TC,CC		31.391,49.9319,37.6711	,	265/351,	99007623	4898,8104	2202	4299	6501	SO:0001583	missense	121457	exon3			TGTCACCTTCTAA	AJ539425	CCDS9067.1, CCDS9068.1, CCDS41822.1	12q23.1	2010-02-17			ENSG00000166130	ENSG00000166130			26430	protein-coding gene	gene with protein product	"""I kappa B kinase interacting protein"""	609861				15389287	Standard	NM_153687		Approved	FLJ31051, IKIP	uc001tfx.4	Q70UQ0	OTTHUMG00000170213	ENST00000342502.2:c.793G>A	12.37:g.99007623C>T	ENSP00000343471:p.Gly265Ser	Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	134	6	0.0447761	NM_201612	Q6ZWH4|Q70UP9|Q86V91|Q96ND2	Missense_Mutation	SNP	ENST00000342502.2	37	CCDS9067.1	779	0.3566849816849817	243	0.49390243902439024	120	0.3314917127071823	187	0.3269230769230769	229	0.3021108179419525	T	1.750	-0.489406	0.04352	0.499319	0.31391	ENSG00000166130	ENST00000342502;ENST00000420861	T;T	0.38077	1.16;1.3	5.54	1.86	0.25419	.	.	.	.	.	T	0.00012	0.0000	N	0.03608	-0.345	0.50632	P	1.1099999999997223E-4	B	0.02656	0.0	B	0.04013	0.001	T	0.47837	-0.9086	8	0.02654	T	1	.	9.8834	0.41247	0.0:0.3942:0.0:0.6058	rs1048906;rs3168530;rs17846476;rs17859535;rs59586369;rs1048906	265	Q70UQ0	IKIP_HUMAN	S	265;159	ENSP00000343471:G265S;ENSP00000398023:G159S	ENSP00000343471:G265S	G	-	1	0	IKBIP	97531754	1.000000	0.71417	1.000000	0.80357	0.774000	0.43823	1.688000	0.37690	0.061000	0.16311	-1.213000	0.01624	GGT	C|0.625;T|0.374	0.374	strong		0.358	IKBIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000408003.2	NM_153687	
DAGLA	747	hgsc.bcm.edu	37	11	61505168	61505168	+	Silent	SNP	G	G	A	rs198444	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr11:61505168G>A	ENST00000257215.5	+	15	1640	c.1524G>A	c.(1522-1524)gcG>gcA	p.A508A		NM_006133.2	NP_006124.1	Q9Y4D2	DGLA_HUMAN	diacylglycerol lipase, alpha	508					arachidonic acid metabolic process (GO:0019369)|blood coagulation (GO:0007596)|cell death (GO:0008219)|diacylglycerol catabolic process (GO:0046340)|endocannabinoid signaling pathway (GO:0071926)|neuroblast proliferation (GO:0007405)|neurotransmitter biosynthetic process (GO:0042136)|platelet activation (GO:0030168)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|liver(2)|lung(17)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(4)	43				READ - Rectum adenocarcinoma(4;0.219)		GTGAGGATGCGATGGAGTATT	0.622													G|||	2461	0.491414	0.3631	0.4986	5008	,	,		15387	0.7986		0.4284	False		,,,				2504	0.408				p.A508A		Atlas-SNP	.											DAGLA,NS,carcinoma,+1,1	DAGLA	109	1	0			c.G1524A						scavenged	.	G		1586,2818	492.9+/-362.5	275,1036,891	160.0	131.0	141.0		1524	-3.4	1.0	11	dbSNP_79	141	3767,4831	535.2+/-382.8	819,2129,1351	no	coding-synonymous	DAGLA	NM_006133.2		1094,3165,2242	AA,AG,GG		43.8125,36.0127,41.1706		508/1043	61505168	5353,7649	2202	4299	6501	SO:0001819	synonymous_variant	747	exon15			GGATGCGATGGAG	AB014559	CCDS31578.1	11q12.3	2008-03-18	2007-02-28	2007-02-28		ENSG00000134780	3.1.1.-		1165	protein-coding gene	gene with protein product	"""neural stem cell-derived dendrite regulator"""	614015	"""chromosome 11 open reading frame 11"""	C11orf11		9734811	Standard	NM_006133		Approved	KIAA0659, NSDDR, DAGLALPHA	uc001nsa.3	Q9Y4D2		ENST00000257215.5:c.1524G>A	11.37:g.61505168G>A		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	105	4	0.0380952	NM_006133	A7E233|Q6WQJ0	Silent	SNP	ENST00000257215.5	37	CCDS31578.1																																																																																			G|0.536;A|0.464	0.464	strong		0.622	DAGLA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398516.1	NM_006133	
CFAP57	149465	hgsc.bcm.edu	37	1	43652442	43652442	+	Missense_Mutation	SNP	G	G	C	rs11210805	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr1:43652442G>C	ENST00000372492.4	+	6	1358	c.1034G>C	c.(1033-1035)tGc>tCc	p.C345S	WDR65_ENST00000528956.1_Missense_Mutation_p.C345S	NM_001195831.2	NP_001182760.2	Q96MR6	WDR65_HUMAN		345			C -> S (in dbSNP:rs11210805).							NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(7)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	23	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)				CTCTGCCTGTGCTTCAGCCCC	0.507													G|||	643	0.128395	0.0098	0.1888	5008	,	,		16964	0.3175		0.0457	False		,,,				2504	0.136				p.C345S		Atlas-SNP	.											.	WDR65	76	.	0			c.G1034C						PASS	.	G	SER/CYS,SER/CYS,SER/CYS	78,4328	69.2+/-107.0	0,78,2125	121.0	106.0	111.0		1034,1034,1034	5.7	1.0	1	dbSNP_120	111	433,8167	133.5+/-191.0	10,413,3877	yes	missense,missense,missense	WDR65	NM_001167965.1,NM_001167966.1,NM_152498.3	112,112,112	10,491,6002	CC,CG,GG		5.0349,1.7703,3.929	possibly-damaging,possibly-damaging,possibly-damaging	345/699,345/699,345/699	43652442	511,12495	2203	4300	6503	SO:0001583	missense	149465	exon6			GCCTGTGCTTCAG																												ENST00000372492.4:c.1034G>C	1.37:g.43652442G>C	ENSP00000361570:p.Cys345Ser	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	52	5	0.0961538	NM_152498	A6NKQ3|Q17RI9|Q5TAI0	Missense_Mutation	SNP	ENST00000372492.4	37		270	0.12362637362637363	10	0.02032520325203252	54	0.14917127071823205	169	0.29545454545454547	37	0.048812664907651716	G	16.51	3.143401	0.57044	0.017703	0.050349	ENSG00000243710	ENST00000372492;ENST00000528956	T;T	0.06849	3.25;3.25	5.67	5.67	0.87782	WD40/YVTN repeat-like-containing domain (1);Quinonprotein alcohol dehydrogenase-like (1);WD40 repeat-like-containing domain (1);	0.047660	0.85682	N	0.000000	T	0.00012	0.0000	M	0.71581	2.175	0.21105	P	0.999789461	B;B	0.33637	0.002;0.42	B;B	0.39876	0.008;0.312	T	0.53940	-0.8367	9	0.19590	T	0.45	.	16.0573	0.80814	0.0:0.134:0.866:0.0	rs11210805	345;345	Q96MR6;Q96MR6-2	WDR65_HUMAN;.	S	345	ENSP00000361570:C345S;ENSP00000435310:C345S	ENSP00000361570:C345S	C	+	2	0	WDR65	43425029	1.000000	0.71417	1.000000	0.80357	0.881000	0.50899	6.082000	0.71318	2.649000	0.89929	0.655000	0.94253	TGC	G|0.929;C|0.071	0.071	strong		0.507	WDR65-002	NOVEL	not_organism_supported|basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000384325.1		
WNT9A	7483	hgsc.bcm.edu	37	1	228109471	228109471	+	Silent	SNP	C	C	T	rs8192633	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr1:228109471C>T	ENST00000272164.5	-	4	856	c.846G>A	c.(844-846)ccG>ccA	p.P282P		NM_003395.2	NP_003386.1	O14904	WNT9A_HUMAN	wingless-type MMTV integration site family, member 9A	282					canonical Wnt signaling pathway (GO:0060070)|cell fate commitment (GO:0045165)|cell-cell signaling (GO:0007267)|cellular response to retinoic acid (GO:0071300)|cornea development in camera-type eye (GO:0061303)|embryonic forelimb morphogenesis (GO:0035115)|embryonic skeletal joint development (GO:0072498)|embryonic skeletal system morphogenesis (GO:0048704)|iris morphogenesis (GO:0061072)|mitotic cell cycle checkpoint (GO:0007093)|multicellular organismal development (GO:0007275)|negative regulation of cartilage development (GO:0061037)|negative regulation of cell death (GO:0060548)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|neuron differentiation (GO:0030182)|positive regulation of cell differentiation (GO:0045597)|positive regulation of smoothened signaling pathway (GO:0045880)|Wnt signaling pathway (GO:0016055)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	frizzled binding (GO:0005109)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(5)|ovary(2)|pancreas(1)|prostate(2)|skin(1)	19		Prostate(94;0.0405)				TGCGGGGCAGCGGGTCGCTGC	0.711													C|||	82	0.0163738	0.0023	0.0086	5008	,	,		14842	0.0		0.0278	False		,,,				2504	0.046				p.P282P		Atlas-SNP	.											.	WNT9A	39	.	0			c.G846A						PASS	.	C		24,4378	29.0+/-57.7	0,24,2177	26.0	28.0	27.0		846	-9.3	0.0	1	dbSNP_117	27	180,8412	78.6+/-141.3	2,176,4118	no	coding-synonymous	WNT9A	NM_003395.2		2,200,6295	TT,TC,CC		2.095,0.5452,1.57		282/366	228109471	204,12790	2201	4296	6497	SO:0001819	synonymous_variant	7483	exon4			GGGCAGCGGGTCG	AB060283	CCDS31045.1	1q42	2008-02-05	2003-03-11	2003-03-14	ENSG00000143816	ENSG00000143816		"""Wingless-type MMTV integration sites"""	12778	protein-coding gene	gene with protein product		602863	"""wingless-type MMTV integration site family, member 14"""	WNT14		9441749	Standard	NM_003395		Approved		uc001hri.2	O14904	OTTHUMG00000037592	ENST00000272164.5:c.846G>A	1.37:g.228109471C>T		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	44	20	0.454545	NM_003395	A6NLW2|Q2M2J3|Q5VWU0|Q96S50	Silent	SNP	ENST00000272164.5	37	CCDS31045.1																																																																																			C|0.985;T|0.015	0.015	strong		0.711	WNT9A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091646.1	NM_003395	
KRTAP5-5	439915	hgsc.bcm.edu	37	11	1651615	1651615	+	Missense_Mutation	SNP	A	A	G	rs576867883|rs74396270|rs71025765		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr11:1651615A>G	ENST00000399676.2	+	1	583	c.545A>G	c.(544-546)tAc>tGc	p.Y182C		NM_001001480.2	NP_001001480.2	Q701N2	KRA55_HUMAN	keratin associated protein 5-5	182	8 X 4 AA repeats of C-C-X-P.			Missing (in Ref. 1; BAD20201 and 2; CAF31639). {ECO:0000305}.		keratin filament (GO:0045095)		p.Y182_P191delYCCQSSCCKP(1)|p.Y192_P201delYCCQSSCCKP(1)		endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(17)|ovary(2)|prostate(5)|urinary_tract(1)	33		all_epithelial(84;0.00018)|Ovarian(85;0.0014)|Breast(177;0.00147)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.000614)|Lung(200;0.0681)|LUSC - Lung squamous cell carcinoma(625;0.082)		TGTAAGCCTTACTGCTGCCAG	0.592																																					p.Y182C		Atlas-SNP	.											KRTAP5-5,NS,carcinoma,0,3	KRTAP5-5	86	3	2	Deletion - In frame(2)	urinary_tract(1)|ovary(1)	c.A545G						scavenged	.						65.0	74.0	71.0					11																	1651615		2200	4292	6492	SO:0001583	missense	439915	exon1			AGCCTTACTGCTG	AB125074	CCDS41592.1	11p15.5	2008-10-30			ENSG00000185940	ENSG00000185940		"""Keratin associated proteins"""	23601	protein-coding gene	gene with protein product						15144888	Standard	NM_001001480		Approved	KRTAP5.5, KRTAP5-11	uc001lty.3	Q701N2	OTTHUMG00000057554	ENST00000399676.2:c.545A>G	11.37:g.1651615A>G	ENSP00000382584:p.Tyr182Cys	Somatic	33	3	0.0909091		WXS	Illumina HiSeq	Phase_I	45	7	0.155556	NM_001001480	A8MWN2	Missense_Mutation	SNP	ENST00000399676.2	37	CCDS41592.1	.	.	.	.	.	.	.	.	.	.	a	0.771	-0.765830	0.02974	.	.	ENSG00000185940	ENST00000399676;ENST00000422553	T	0.01335	5.0	3.69	0.448	0.16614	.	.	.	.	.	T	0.00496	0.0016	N	0.00453	-1.485	0.58432	P	5.000000000032756E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.44065	-0.9352	8	0.37606	T	0.19	.	3.2614	0.06850	0.1044:0.1706:0.5496:0.1753	.	182	Q701N2	KRA55_HUMAN	C	182;153	ENSP00000382584:Y182C	ENSP00000382584:Y182C	Y	+	2	0	KRTAP5-5	1608191	0.006000	0.16342	0.000000	0.03702	0.003000	0.03518	1.388000	0.34442	-0.252000	0.09528	-0.366000	0.07423	TAC	.	.	weak		0.592	KRTAP5-5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127919.1		
G6PC3	92579	hgsc.bcm.edu	37	17	42152103	42152103	+	Silent	SNP	G	G	A	rs3815076	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr17:42152103G>A	ENST00000269097.4	+	3	612	c.381G>A	c.(379-381)acG>acA	p.T127T		NM_138387.3	NP_612396.1	Q9BUM1	G6PC3_HUMAN	glucose 6 phosphatase, catalytic, 3	127					carbohydrate metabolic process (GO:0005975)|gluconeogenesis (GO:0006094)|glucose 6-phosphate metabolic process (GO:0051156)|glucose transport (GO:0015758)|glucose-6-phosphate transport (GO:0015760)|hexose transport (GO:0008645)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	glucose-6-phosphatase activity (GO:0004346)			endometrium(2)|large_intestine(5)|lung(1)|ovary(2)|skin(1)	11		Breast(137;0.00637)|Prostate(33;0.0313)		BRCA - Breast invasive adenocarcinoma(366;0.113)		CCATAATGACGGCCCTGTCTT	0.587													G|||	1352	0.269968	0.0908	0.3213	5008	,	,		18006	0.7093		0.0825	False		,,,				2504	0.2157				p.T127T		Atlas-SNP	.											.	G6PC3	26	.	0			c.G381A						PASS	.	G		469,3937	219.7+/-237.4	28,413,1762	39.0	38.0	38.0		381	-10.1	0.2	17	dbSNP_107	38	641,7959	163.5+/-216.0	27,587,3686	no	coding-synonymous	G6PC3	NM_138387.3		55,1000,5448	AA,AG,GG		7.4535,10.6446,8.5345		127/347	42152103	1110,11896	2203	4300	6503	SO:0001819	synonymous_variant	92579	exon3			AATGACGGCCCTG	BC021574	CCDS11476.1	17q21.31	2014-09-17				ENSG00000141349			24861	protein-coding gene	gene with protein product		611045				12370122, 12965222	Standard	NM_138387		Approved	UGRP	uc002iex.3	Q9BUM1		ENST00000269097.4:c.381G>A	17.37:g.42152103G>A		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	43	6	0.139535	NM_138387	Q8WU15	Silent	SNP	ENST00000269097.4	37	CCDS11476.1																																																																																			G|0.834;A|0.166	0.166	strong		0.587	G6PC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457675.1	NM_138387	
TTN	7273	hgsc.bcm.edu	37	2	179640650	179640650	+	Missense_Mutation	SNP	T	T	C			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr2:179640650T>C	ENST00000591111.1	-	28	6165	c.5941A>G	c.(5941-5943)Agg>Ggg	p.R1981G	TTN-AS1_ENST00000584485.1_RNA|TTN-AS1_ENST00000610005.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.R1935G|TTN_ENST00000589042.1_Missense_Mutation_p.R1981G|TTN_ENST00000360870.5_Missense_Mutation_p.R1981G|RP11-88L24.4_ENST00000582038.2_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.R1981G|TTN_ENST00000359218.5_Missense_Mutation_p.R1935G|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.R1935G			Q8WZ42	TITIN_HUMAN	titin	12802					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)			CTTTCAGCCCTTTTCAACTTC	0.423																																					p.R1981G		Atlas-SNP	.											TTN_ENST00000360870,NS,carcinoma,+2,6	TTN	18412	6	0			c.A5941G						scavenged	.						141.0	146.0	144.0					2																	179640650		2203	4300	6503	SO:0001583	missense	7273	exon28			CAGCCCTTTTCAA	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.5941A>G	2.37:g.179640650T>C	ENSP00000465570:p.Arg1981Gly	Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	135	4	0.0296296	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		.	.	.	.	.	.	.	.	.	.	T	11.21	1.572810	0.28092	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127;ENST00000360870	T;T;T;T;T	0.64260	-0.09;0.16;0.15;0.14;0.29	5.1	5.1	0.69264	Ribonuclease H-like (1);	.	.	.	.	T	0.59555	0.2202	N	0.19112	0.55	0.31118	N	0.709203	P;P;P;P;P	0.52316	0.651;0.651;0.651;0.651;0.952	B;B;B;B;P	0.51701	0.165;0.165;0.165;0.165;0.677	T	0.66085	-0.6011	9	0.87932	D	0	.	14.8848	0.70560	0.0:0.0:0.0:1.0	.	1935;1935;1935;1981;1981	D3DPF9;E7EQE6;E7ET18;Q8WZ42;Q8WZ42-6	.;.;.;TITIN_HUMAN;.	G	1981;1935;1935;1935;1935;1981	ENSP00000343764:R1981G;ENSP00000434586:R1935G;ENSP00000340554:R1935G;ENSP00000352154:R1935G;ENSP00000354117:R1981G	ENSP00000340554:R1935G	R	-	1	2	TTN	179348895	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	6.163000	0.71880	1.932000	0.55993	0.496000	0.49642	AGG	.	.	none		0.423	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
ZNF318	24149	hgsc.bcm.edu	37	6	43305520	43305520	+	Silent	SNP	C	C	T	rs35650765	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr6:43305520C>T	ENST00000361428.2	-	10	6293	c.6216G>A	c.(6214-6216)ccG>ccA	p.P2072P	ZNF318_ENST00000318149.3_Intron	NM_014345.2	NP_055160.2	Q5VUA4	ZN318_HUMAN	zinc finger protein 318	2072					meiotic nuclear division (GO:0007126)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(8)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(21)|ovary(3)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	61			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0171)|OV - Ovarian serous cystadenocarcinoma(102;0.0579)			GAGAATCTAACGGAAACCCAG	0.443													C|||	94	0.01877	0.003	0.0202	5008	,	,		20560	0.0129		0.0487	False		,,,				2504	0.0143				p.P2072P		Atlas-SNP	.											ZNF318,colon,carcinoma,0,1	ZNF318	175	1	0			c.G6216A						scavenged	.	C		40,4366	44.6+/-78.6	0,40,2163	80.0	76.0	78.0		6216	-11.7	0.2	6	dbSNP_126	78	413,8187	130.0+/-188.0	10,393,3897	no	coding-synonymous	ZNF318	NM_014345.2		10,433,6060	TT,TC,CC		4.8023,0.9079,3.483		2072/2280	43305520	453,12553	2203	4300	6503	SO:0001819	synonymous_variant	24149	exon10			ATCTAACGGAAAC	AF090114	CCDS4895.2	6p21.1	2013-09-19			ENSG00000171467	ENSG00000171467		"""Zinc fingers, C2H2-type"""	13578	protein-coding gene	gene with protein product						10873617	Standard	NM_014345		Approved	HRIHFB2436, ZFP318	uc003oux.3	Q5VUA4	OTTHUMG00000014732	ENST00000361428.2:c.6216G>A	6.37:g.43305520C>T		Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	194	5	0.0257732	NM_014345	O94796|Q4G0E4|Q8NEM6|Q9UNU8|Q9Y2W9	Silent	SNP	ENST00000361428.2	37	CCDS4895.2																																																																																			C|0.970;T|0.030	0.030	strong		0.443	ZNF318-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040601.2	NM_014345	
IL1F10	84639	hgsc.bcm.edu	37	2	113831945	113831945	+	Silent	SNP	T	T	C	rs3811058	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr2:113831945T>C	ENST00000393197.2	+	2	493	c.72T>C	c.(70-72)gaT>gaC	p.D24D	IL1F10_ENST00000337569.3_Intron|IL1F10_ENST00000341010.2_Silent_p.D24D	NM_032556.5	NP_115945.4	Q8WWZ1	IL1FA_HUMAN	interleukin 1 family, member 10 (theta)	24						extracellular space (GO:0005615)				endometrium(1)|lung(6)|ovary(1)	8						ACACAAGAGATGGCCAGCTGC	0.547													T|||	885	0.176717	0.0477	0.1282	5008	,	,		21509	0.5179		0.0795	False		,,,				2504	0.1339				p.D24D		Atlas-SNP	.											.	IL1F10	19	.	0			c.T72C						PASS	.	T	,	248,4158	145.0+/-179.8	8,232,1963	112.0	99.0	104.0		72,72	-8.5	0.0	2	dbSNP_107	104	627,7973	163.0+/-215.7	21,585,3694	no	coding-synonymous,coding-synonymous	IL1F10	NM_032556.5,NM_173161.2	,	29,817,5657	CC,CT,TT		7.2907,5.6287,6.7277	,	24/153,24/153	113831945	875,12131	2203	4300	6503	SO:0001819	synonymous_variant	84639	exon3			AAGAGATGGCCAG	AY026753	CCDS2112.1	2q13	2011-07-14			ENSG00000136697	ENSG00000136697		"""Interleukins and interleukin receptors"""	15552	protein-coding gene	gene with protein product	"""FIL1- theta"", ""interleukin-1 receptor antagonist FKSG75"""	615296				11747621, 11991723, 11991722	Standard	NM_173161		Approved	FKSG75, IL-1HY2, IL-1F10, IL1-theta, MGC11983, MGC119832, MGC119833	uc002tiu.3	Q8WWZ1	OTTHUMG00000131339	ENST00000393197.2:c.72T>C	2.37:g.113831945T>C		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	170	9	0.0529412	NM_173161	Q53SR9|Q56AT8|Q7RTZ5|Q969H5|Q9BYX1	Silent	SNP	ENST00000393197.2	37	CCDS2112.1																																																																																			T|0.891;C|0.109	0.109	strong		0.547	IL1F10-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000330725.1	NM_173161	
DOK7	285489	hgsc.bcm.edu	37	4	3494898	3494898	+	Silent	SNP	C	C	T	rs6850908	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr4:3494898C>T	ENST00000340083.5	+	7	1250	c.1185C>T	c.(1183-1185)taC>taT	p.Y395Y	DOK7_ENST00000512714.1_3'UTR|DOK7_ENST00000507039.1_3'UTR|DOK7_ENST00000389653.2_Silent_p.Y395Y	NM_173660.4	NP_775931.3	Q18PE1	DOK7_HUMAN	docking protein 7	395					neuromuscular junction development (GO:0007528)|positive regulation of protein tyrosine kinase activity (GO:0061098)|receptor clustering (GO:0043113)	cell junction (GO:0030054)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)	phosphatidylinositol binding (GO:0035091)|protein kinase binding (GO:0019901)			kidney(1)|large_intestine(1)|skin(2)|upper_aerodigestive_tract(1)	5				UCEC - Uterine corpus endometrioid carcinoma (64;0.163)		CAGTCGAGTACCAGGTGCCCA	0.692													.|||	1100	0.219649	0.0386	0.1441	5008	,	,		14813	0.502		0.2237	False		,,,				2504	0.2229				p.Y395Y		Atlas-SNP	.											DOK7,NS,carcinoma,0,1	DOK7	44	1	0			c.C1185T						PASS	.	C	,	291,4089		15,261,1914	15.0	15.0	15.0		,1185	2.8	1.0	4	dbSNP_116	15	1780,6802		194,1392,2705	yes	utr-3,coding-synonymous	DOK7	NM_001164673.1,NM_173660.4	,	209,1653,4619	TT,TC,CC		20.7411,6.6438,15.9775	,	,395/505	3494898	2071,10891	2190	4291	6481	SO:0001819	synonymous_variant	285489	exon7			CGAGTACCAGGTG	AK091037	CCDS3370.2, CCDS54717.1	4p16.2	2014-09-17	2006-08-24	2006-08-24	ENSG00000175920	ENSG00000175920			26594	protein-coding gene	gene with protein product		610285	"""chromosome 4 open reading frame 25"""	C4orf25		16794080	Standard	NM_173660		Approved	FLJ33718, FLJ39137, Dok-7	uc003ghd.3	Q18PE1	OTTHUMG00000122087	ENST00000340083.5:c.1185C>T	4.37:g.3494898C>T		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	92	5	0.0543478	NM_173660	A2A499|A2RRD4|E9PB56|Q6P6A6|Q86XG5|Q8N2J3|Q8NBC1	Silent	SNP	ENST00000340083.5	37	CCDS3370.2																																																																																			C|0.794;T|0.206	0.206	strong		0.692	DOK7-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000313538.1	NM_173660	
TBC1D32	221322	hgsc.bcm.edu	37	6	121602795	121602795	+	Silent	SNP	C	C	T	rs79788801	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr6:121602795C>T	ENST00000398212.2	-	14	1552	c.1503G>A	c.(1501-1503)ctG>ctA	p.L501L	TBC1D32_ENST00000275159.6_Silent_p.L501L	NM_152730.4	NP_689943.4	Q96NH3	BROMI_HUMAN	TBC1 domain family, member 32	501					cilium morphogenesis (GO:0060271)|embryonic digit morphogenesis (GO:0042733)|lens development in camera-type eye (GO:0002088)|protein localization to cilium (GO:0061512)|retinal pigment epithelium development (GO:0003406)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)	cilium (GO:0005929)|cytoplasm (GO:0005737)	Rab GTPase activator activity (GO:0005097)	p.L501L(1)									TGAGTATCCACAGAACTTCAG	0.294													T|||	273	0.0545128	0.034	0.1196	5008	,	,		14544	0.124		0.0109	False		,,,				2504	0.0092				p.L501L		Atlas-SNP	.											C6orf170,NS,carcinoma,0,1	C6orf170	146	1	1	Substitution - coding silent(1)	stomach(1)	c.G1503A						scavenged	.	T		107,3537		3,101,1718	95.0	90.0	92.0		1503	-9.2	0.0	6	dbSNP_131	92	95,8049		0,95,3977	no	coding-synonymous	C6orf170	NM_152730.4		3,196,5695	TT,TC,CC		1.1665,2.9363,1.7136		501/1258	121602795	202,11586	1822	4072	5894	SO:0001819	synonymous_variant	221322	exon14			TATCCACAGAACT	AK055461	CCDS43501.1	6q22.31	2014-02-20	2013-07-10	2013-07-10	ENSG00000146350	ENSG00000146350			21485	protein-coding gene	gene with protein product	"""broad-minded homolog"""	615867	"""chromosome 6 open reading frame 171"", ""chromosome 6 open reading frame 170"""	C6orf171, C6orf170		20159594, 24285566	Standard	NM_152730		Approved	FLJ30899, dJ310J6.1, FLJ34235, bA57L9.1, BROMI	uc003pyo.1	Q96NH3	OTTHUMG00000015474	ENST00000398212.2:c.1503G>A	6.37:g.121602795C>T		Somatic	303	1	0.00330033		WXS	Illumina HiSeq	Phase_I	217	8	0.0368664	NM_152730	Q5SZD6|Q5SZM6|Q6ZMY4|Q6ZUR7|Q8NB47	Silent	SNP	ENST00000398212.2	37	CCDS43501.1																																																																																			C|0.954;T|0.046	0.046	strong		0.294	TBC1D32-005	PUTATIVE	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380937.2	NM_152730	
APOH	350	hgsc.bcm.edu	37	17	64210757	64210757	+	Missense_Mutation	SNP	C	C	A	rs4581	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr17:64210757C>A	ENST00000205948.6	-	7	833	c.796G>T	c.(796-798)Gta>Tta	p.V266L		NM_000042.2	NP_000033.2	P02749	APOH_HUMAN	apolipoprotein H (beta-2-glycoprotein I)	266	Sushi-like.		V -> L (in 23% of the population; dbSNP:rs4581). {ECO:0000269|PubMed:8099061, ECO:0000269|Ref.8}.		blood coagulation, intrinsic pathway (GO:0007597)|negative regulation of angiogenesis (GO:0016525)|negative regulation of blood coagulation (GO:0030195)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of myeloid cell apoptotic process (GO:0033033)|negative regulation of smooth muscle cell apoptotic process (GO:0034392)|plasminogen activation (GO:0031639)|positive regulation of blood coagulation (GO:0030194)|positive regulation of lipoprotein lipase activity (GO:0051006)|regulation of fibrinolysis (GO:0051917)|triglyceride metabolic process (GO:0006641)|triglyceride transport (GO:0034197)	cell surface (GO:0009986)|chylomicron (GO:0042627)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|high-density lipoprotein particle (GO:0034364)|very-low-density lipoprotein particle (GO:0034361)	glycoprotein binding (GO:0001948)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|lipid binding (GO:0008289)|lipoprotein lipase activator activity (GO:0060230)|phospholipid binding (GO:0005543)			central_nervous_system(1)|kidney(3)|large_intestine(5)|lung(6)|skin(1)|upper_aerodigestive_tract(1)	17			BRCA - Breast invasive adenocarcinoma(6;9.74e-08)			TTCACAGGTACTTTACAAGAT	0.358													C|||	2712	0.541534	0.5469	0.5403	5008	,	,		19124	0.754		0.2316	False		,,,				2504	0.635				p.V266L	Melanoma(155;624 1882 16869 48804 51309)	Atlas-SNP	.											.	APOH	45	.	0			c.G796T	GRCh37	CM993913	APOH	M	rs4581	PASS	.	C	LEU/VAL	2245,2161	587.0+/-386.6	592,1061,550	101.0	104.0	103.0		796	-4.5	0.4	17	dbSNP_52	103	2043,6557	354.2+/-329.4	232,1579,2489	yes	missense	APOH	NM_000042.2	32	824,2640,3039	AA,AC,CC		23.7558,49.0468,32.9694	benign	266/346	64210757	4288,8718	2203	4300	6503	SO:0001583	missense	350	exon7			CAGGTACTTTACA		CCDS11663.1	17q24.2	2013-01-24				ENSG00000091583		"""Apolipoproteins"""	616	protein-coding gene	gene with protein product	"""beta-2-glycoprotein I"""	138700		B2G1		1582254	Standard	NM_000042		Approved	BG	uc002jfn.4	P02749		ENST00000205948.6:c.796G>T	17.37:g.64210757C>A	ENSP00000205948:p.Val266Leu	Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	140	6	0.0428571	NM_000042	B2R9M3|Q9UCN7	Missense_Mutation	SNP	ENST00000205948.6	37	CCDS11663.1	1035	0.4739010989010989	266	0.540650406504065	166	0.4585635359116022	434	0.7587412587412588	169	0.22295514511873352	c	5.730	0.319109	0.10845	0.509532	0.237558	ENSG00000091583	ENST00000205948	T	0.27720	1.65	5.23	-4.53	0.03462	Complement control module (2);Beta-2-glycoprotein-1 fifth domain (1);	0.357878	0.28322	N	0.015772	T	0.00012	0.0000	N	0.04636	-0.2	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.32161	-0.9917	9	0.08179	T	0.78	.	2.3666	0.04320	0.1613:0.4298:0.1542:0.2548	rs4581;rs1126726;rs1799838;rs3176975;rs3181939;rs17294696;rs17349184;rs52794598;rs56543969;rs60793316;rs3176975	266	P02749	APOH_HUMAN	L	266	ENSP00000205948:V266L	ENSP00000205948:V266L	V	-	1	0	APOH	61641219	0.307000	0.24500	0.356000	0.25785	0.612000	0.37316	-0.386000	0.07370	-0.422000	0.07405	-0.274000	0.10170	GTA	C|0.581;A|0.419	0.419	strong		0.358	APOH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446926.1	NM_000042	
DPP6	1804	hgsc.bcm.edu	37	7	154681050	154681050	+	Silent	SNP	C	C	T	rs1129300	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr7:154681050C>T	ENST00000377770.3	+	24	2514	c.2373C>T	c.(2371-2373)gcC>gcT	p.A791A	DPP6_ENST00000427557.1_Silent_p.A684A|DPP6_ENST00000332007.3_Silent_p.A729A|DPP6_ENST00000404039.1_Silent_p.A727A			P42658	DPP6_HUMAN	dipeptidyl-peptidase 6	791					cell death (GO:0008219)|neuronal action potential (GO:0019228)|positive regulation of potassium ion transmembrane transport (GO:1901381)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	dipeptidyl-peptidase activity (GO:0008239)|serine-type peptidase activity (GO:0008236)	p.A727A(1)		NS(3)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(4)|lung(35)|pancreas(4)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	71	all_neural(206;0.181)	all_hematologic(28;0.0044)|all_lung(21;0.0176)|Lung NSC(21;0.0204)	OV - Ovarian serous cystadenocarcinoma(82;0.0562)			ATCCCACTGCCGATGGTAAGG	0.483													C|||	808	0.161342	0.0053	0.0922	5008	,	,		19575	0.4673		0.1074	False		,,,				2504	0.1616				p.A791A	NSCLC(125;1384 1783 2490 7422 34254)	Atlas-SNP	.											DPP6,NS,carcinoma,0,1	DPP6	383	1	1	Substitution - coding silent(1)	stomach(1)	c.C2373T						scavenged	.	C	,,	106,3898		0,106,1896	53.0	54.0	54.0		1827,1746,1746	-9.0	0.0	7	dbSNP_86	54	965,7381		50,865,3258	no	coding-synonymous,coding-synonymous,coding-synonymous	DPP6	NM_001039350.1,NM_001936.3,NM_130797.2	,,	50,971,5154	TT,TC,CC		11.5624,2.6474,8.6721	,,	609/684,582/657,582/657	154681050	1071,11279	2002	4173	6175	SO:0001819	synonymous_variant	1804	exon24			CACTGCCGATGGT	M96859	CCDS75682.1, CCDS75683.1, CCDS75684.1	7q36.2	2006-08-07	2006-01-12		ENSG00000130226	ENSG00000130226			3010	protein-coding gene	gene with protein product		126141	"""dipeptidylpeptidase VI"", ""dipeptidylpeptidase 6"""			1729689	Standard	XM_006715871		Approved	DPPX	uc003wlk.3	P42658	OTTHUMG00000151511	ENST00000377770.3:c.2373C>T	7.37:g.154681050C>T		Somatic	121	1	0.00826446		WXS	Illumina HiSeq	Phase_I	70	5	0.0714286	NM_130797		Silent	SNP	ENST00000377770.3	37																																																																																				C|0.837;G|0.000;T|0.163	0.163	strong		0.483	DPP6-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000322932.1	NM_130797	
ANKUB1	389161	hgsc.bcm.edu	37	3	149479301	149479301	+	IGR	SNP	C	C	T	rs954714	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr3:149479301C>T	ENST00000383050.3	-	0	1732				ANKUB1_ENST00000446160.1_Silent_p.A535A			A6NFN9	ANKUB_HUMAN	ankyrin repeat and ubiquitin domain containing 1									p.A535A(1)		breast(1)|kidney(1)|lung(1)|skin(1)	4						AGTTTTCACACGCTGTCAGAC	0.408													T|||	2607	0.520567	0.6543	0.402	5008	,	,		18894	0.5139		0.4911	False		,,,				2504	0.4611				p.A535A		Atlas-SNP	.											ANKUB1,NS,carcinoma,0,1	ANKUB1	27	1	1	Substitution - coding silent(1)	kidney(1)	c.G1605A						PASS	.						152.0	128.0	136.0					3																	149479301		692	1591	2283	SO:0001628	intergenic_variant	389161	exon6			TTCACACGCTGTC	AK027233		3q25.1	2013-01-11	2011-05-10	2011-05-10	ENSG00000206199	ENSG00000206199		"""Ankyrin repeat domain containing"""	29642	protein-coding gene	gene with protein product			"""chromosome 3 open reading frame 16"""	C3orf16			Standard	NM_001144960		Approved		uc003exl.3	A6NFN9	OTTHUMG00000159615		3.37:g.149479301C>T		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	95	5	0.0526316	NM_001144960	B4E2N8	Silent	SNP	ENST00000383050.3	37																																																																																				C|0.444;T|0.556	0.556	strong		0.408	ANKUB1-201	KNOWN	basic	protein_coding	protein_coding		NM_001144960	
PRB3	5544	hgsc.bcm.edu	37	12	11420904	11420904	+	Silent	SNP	T	T	C	rs541681122		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr12:11420904T>C	ENST00000279573.7	-	3	414	c.279A>G	c.(277-279)ccA>ccG	p.P93P	PRB3_ENST00000381842.3_Silent_p.P93P|PRB3_ENST00000538488.1_Silent_p.P93P|PRB3_ENST00000440870.3_Intron			Q04118	PRB3_HUMAN	proline-rich protein BstNI subfamily 3	93	10 X 21 AA tandem repeats of [RH]-P-G-K- P-[EQ]-G-[PQS]-P-[PS]-Q-[GE]-G-N-[QK]- [SP]-[QR]-[GR]-P-P-P.|Pro-rich.				defense response to Gram-negative bacterium (GO:0050829)	extracellular region (GO:0005576)				breast(2)|endometrium(1)|kidney(2)|large_intestine(1)|lung(13)|ovary(1)|skin(5)	25			OV - Ovarian serous cystadenocarcinoma(49;0.201)			CCGGACGAGGTGGGGGACCTT	0.632																																					p.P93P		Atlas-SNP	.											PRB3_ENST00000538488,colon,carcinoma,0,2	PRB3	84	2	0			c.A279G						scavenged	.						144.0	180.0	168.0					12																	11420904		2084	4222	6306	SO:0001819	synonymous_variant	5544	exon3			ACGAGGTGGGGGA			12p13.2	2012-10-02				ENSG00000197870			9339	protein-coding gene	gene with protein product		168840				1894623	Standard	NM_006249		Approved	PRG	uc001qzs.3	Q04118		ENST00000279573.7:c.279A>G	12.37:g.11420904T>C		Somatic	27	5	0.185185		WXS	Illumina HiSeq	Phase_I	40	8	0.2	NM_006249	Q15188|Q4VAY3|Q4VAY4|Q7M4M9|Q9UCT9	Silent	SNP	ENST00000279573.7	37																																																																																				.	.	none		0.632	PRB3-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000402119.5	NM_006249	
VWDE	221806	hgsc.bcm.edu	37	7	12395813	12395813	+	Silent	SNP	T	T	C	rs2119141	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr7:12395813T>C	ENST00000275358.3	-	18	3857	c.3669A>G	c.(3667-3669)caA>caG	p.Q1223Q		NM_001135924.1	NP_001129396.1	Q8N2E2	VWDE_HUMAN	von Willebrand factor D and EGF domains	1223						extracellular region (GO:0005576)				breast(4)|endometrium(2)|kidney(1)|skin(1)	8						AAGGGTTGGATTGGCACCCAC	0.463													T|||	3860	0.770767	0.7171	0.7939	5008	,	,		14767	0.8065		0.7316	False		,,,				2504	0.8303				p.Q1223Q		Atlas-SNP	.											.	VWDE	123	.	0			c.A3669G						PASS	.	T		1021,363		385,251,56	95.0	82.0	86.0		3669	-7.7	0.0	7	dbSNP_96	86	2352,830		875,602,114	no	coding-synonymous	VWDE	NM_001135924.1		1260,853,170	CC,CT,TT		26.0842,26.2283,26.1279		1223/1591	12395813	3373,1193	692	1591	2283	SO:0001819	synonymous_variant	221806	exon18			GTTGGATTGGCAC		CCDS47544.1	7p21.3	2008-09-23			ENSG00000146530	ENSG00000146530			21897	protein-coding gene	gene with protein product						14702039, 16303743	Standard	NM_001135924		Approved	FLJ14712	uc003ssj.2	Q8N2E2	OTTHUMG00000152315	ENST00000275358.3:c.3669A>G	7.37:g.12395813T>C		Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	169	9	0.0532544	NM_001135924	B7ZM77|Q96SQ3	Silent	SNP	ENST00000275358.3	37	CCDS47544.1																																																																																			T|0.258;C|0.742	0.742	strong		0.463	VWDE-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325870.3	XM_371878	
NEIL3	55247	hgsc.bcm.edu	37	4	178274835	178274835	+	Missense_Mutation	SNP	A	A	C	rs13112390	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr4:178274835A>C	ENST00000264596.3	+	8	1531	c.1413A>C	c.(1411-1413)caA>caC	p.Q471H	RP11-376O6.2_ENST00000506895.1_RNA	NM_018248.2	NP_060718	Q8TAT5	NEIL3_HUMAN	nei endonuclease VIII-like 3 (E. coli)	471			Q -> H (in dbSNP:rs13112390). {ECO:0000269|PubMed:12200441, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.3}.		base-excision repair (GO:0006284)|DNA catabolic process, endonucleolytic (GO:0000737)|nucleotide-excision repair (GO:0006289)	nucleus (GO:0005634)	bubble DNA binding (GO:0000405)|damaged DNA binding (GO:0003684)|DNA N-glycosylase activity (GO:0019104)|DNA-(apurinic or apyrimidinic site) lyase activity (GO:0003906)|double-stranded DNA binding (GO:0003690)|single-stranded DNA binding (GO:0003697)|zinc ion binding (GO:0008270)	p.Q471H(1)		breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(14)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	29		Breast(14;6.27e-05)|Melanoma(52;0.00102)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|all_neural(102;0.164)		all cancers(43;1.96e-23)|Epithelial(43;2.52e-20)|OV - Ovarian serous cystadenocarcinoma(60;1.89e-11)|GBM - Glioblastoma multiforme(59;9.49e-05)|Colorectal(24;0.00013)|COAD - Colon adenocarcinoma(29;0.000696)|STAD - Stomach adenocarcinoma(60;0.00308)|LUSC - Lung squamous cell carcinoma(193;0.0398)|READ - Rectum adenocarcinoma(43;0.191)		AAACAGCCCAATACTCATCAC	0.333								Base excision repair (BER), DNA glycosylases					C|||	3318	0.66254	0.7118	0.7089	5008	,	,		17353	0.4474		0.8022	False		,,,				2504	0.6411				p.Q471H		Atlas-SNP	.											NEIL3_ENST00000264596,colon,carcinoma,0,2	NEIL3	89	2	1	Substitution - Missense(1)	prostate(1)	c.A1413C						scavenged	.	C	HIS/GLN	3197,1209	417.2+/-337.8	1167,863,173	70.0	70.0	70.0		1413	-1.1	0.0	4	dbSNP_121	70	6832,1768	317.8+/-313.4	2704,1424,172	yes	missense	NEIL3	NM_018248.2	24	3871,2287,345	CC,CA,AA		20.5581,27.4399,22.8894	benign	471/606	178274835	10029,2977	2203	4300	6503	SO:0001583	missense	55247	exon8			AGCCCAATACTCA	AB079071	CCDS3828.1	4q34	2014-02-18			ENSG00000109674	ENSG00000109674			24573	protein-coding gene	gene with protein product	"""zinc finger, GRF-type containing 3"""	608934				12713815, 12509226	Standard	NM_018248		Approved	FLJ10858, hFPG2, FPG2, hNEI3, ZGRF3	uc003iut.2	Q8TAT5	OTTHUMG00000160722	ENST00000264596.3:c.1413A>C	4.37:g.178274835A>C	ENSP00000264596:p.Gln471His	Somatic	350	3	0.00857143		WXS	Illumina HiSeq	Phase_I	259	7	0.027027	NM_018248	Q2PPJ3|Q8NG51|Q9NV95	Missense_Mutation	SNP	ENST00000264596.3	37	CCDS3828.1	1469	0.6726190476190477	345	0.7012195121951219	269	0.7430939226519337	250	0.4370629370629371	605	0.7981530343007915	C	0.051	-1.250706	0.01469	0.725601	0.794419	ENSG00000109674	ENST00000264596	T	0.03772	3.81	3.8	-1.15	0.09709	.	0.221814	0.46442	N	0.000290	T	0.00012	0.0000	N	0.00182	-1.905	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.10474	-1.0628	9	0.07482	T	0.82	-1.0524	1.4023	0.02273	0.1226:0.3235:0.2407:0.3131	rs13112390;rs17845786;rs17858747;rs52821314;rs58437627;rs13112390	471	Q8TAT5	NEIL3_HUMAN	H	471	ENSP00000264596:Q471H	ENSP00000264596:Q471H	Q	+	3	2	NEIL3	178511829	0.002000	0.14202	0.003000	0.11579	0.040000	0.13550	-0.182000	0.09726	-0.566000	0.06054	-0.224000	0.12420	CAA	A|0.289;C|0.711	0.711	strong		0.333	NEIL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361914.1	NM_018248	
LACTB	114294	hgsc.bcm.edu	37	15	63433785	63433785	+	Silent	SNP	G	G	A	rs4775629	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr15:63433785G>A	ENST00000261893.4	+	6	1497	c.1425G>A	c.(1423-1425)tcG>tcA	p.S475S	RPS27L_ENST00000559763.1_Intron	NM_032857.3	NP_116246.2	P83111	LACTB_HUMAN	lactamase, beta	475						cytoplasm (GO:0005737)|mitochondrion (GO:0005739)	hydrolase activity (GO:0016787)	p.S475S(1)		NS(1)|breast(1)|kidney(1)|large_intestine(3)|lung(3)|prostate(1)|skin(1)|stomach(1)	12						CGTATGGTTCGTGTAGAAAGC	0.483													G|||	615	0.122804	0.1921	0.0922	5008	,	,		20324	0.1677		0.0308	False		,,,				2504	0.0992				p.S475S	Melanoma(85;443 1381 6215 27308 35583)	Atlas-SNP	.											LACTB,NS,carcinoma,0,1	LACTB	29	1	1	Substitution - coding silent(1)	stomach(1)	c.G1425A						scavenged	.	G		735,3671	304.1+/-288.3	72,591,1540	77.0	67.0	70.0		1425	-5.8	0.9	15	dbSNP_111	70	206,8394	88.6+/-150.9	2,202,4096	no	coding-synonymous	LACTB	NM_032857.3		74,793,5636	AA,AG,GG		2.3953,16.6818,7.2351		475/548	63433785	941,12065	2203	4300	6503	SO:0001819	synonymous_variant	114294	exon6			TGGTTCGTGTAGA	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.1425G>A	15.37:g.63433785G>A		Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	142	4	0.028169	NM_032857	P83096	Silent	SNP	ENST00000261893.4	37	CCDS10182.1																																																																																			G|0.904;A|0.096	0.096	strong		0.483	LACTB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256224.1	NM_032857	
DSPP	1834	hgsc.bcm.edu	37	4	88537078	88537078	+	Silent	SNP	T	T	C	rs367717407|rs373805744	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr4:88537078T>C	ENST00000282478.7	+	4	3297	c.3264T>C	c.(3262-3264)agT>agC	p.S1088S	DSPP_ENST00000399271.1_Silent_p.S1088S|RP11-742B18.1_ENST00000506480.1_RNA			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	1088	Asp/Ser-rich.				biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|skin(3)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		gtgatagcagtgacagcagca	0.547													t|||	1148	0.229233	0.27	0.2536	5008	,	,		14971	0.2103		0.2237	False		,,,				2504	0.182				p.S1088S		Atlas-SNP	.											DSPP,colon,carcinoma,0,1	DSPP	174	1	0			c.T3264C						scavenged	.						21.0	26.0	24.0					4																	88537078		1113	2064	3177	SO:0001819	synonymous_variant	1834	exon5			TAGCAGTGACAGC	AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.3264T>C	4.37:g.88537078T>C		Somatic	21	6	0.285714		WXS	Illumina HiSeq	Phase_I	57	24	0.421053	NM_014208	A8MUI0|O95815	Silent	SNP	ENST00000282478.7	37	CCDS43248.1																																																																																			.	.	weak		0.547	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208	
SVEP1	79987	hgsc.bcm.edu	37	9	113192655	113192655	+	Missense_Mutation	SNP	T	T	G	rs2986671	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr9:113192655T>G	ENST00000401783.2	-	33	5765	c.5429A>C	c.(5428-5430)gAa>gCa	p.E1810A	SVEP1_ENST00000297826.5_5'Flank|SVEP1_ENST00000374469.1_Missense_Mutation_p.E1787A	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	1810	Sushi 7. {ECO:0000255|PROSITE- ProRule:PRU00302}.		E -> A (in dbSNP:rs2986671).		cell adhesion (GO:0007155)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|chromatin binding (GO:0003682)	p.E1813A(1)		NS(1)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|cervix(2)|endometrium(19)|kidney(8)|large_intestine(24)|lung(58)|ovary(7)|prostate(7)|skin(1)|stomach(4)|upper_aerodigestive_tract(5)|urinary_tract(4)	147						AAATGTGACTTCGGCACCTAC	0.408													T|||	930	0.185703	0.0129	0.2406	5008	,	,		17798	0.4087		0.1829	False		,,,				2504	0.1534				p.E1810A		Atlas-SNP	.											SVEP1,NS,carcinoma,-1,3	SVEP1	326	3	1	Substitution - Missense(1)	stomach(1)	c.A5429C						scavenged	.	T	ALA/GLU	137,3617		3,131,1743	68.0	61.0	63.0		5429	2.8	0.0	9	dbSNP_101	63	1400,6836		119,1162,2837	yes	missense	SVEP1	NM_153366.3	107	122,1293,4580	GG,GT,TT		16.9985,3.6494,12.819	benign	1810/3572	113192655	1537,10453	1877	4118	5995	SO:0001583	missense	79987	exon33			GTGACTTCGGCAC	AK027870		9q31-q32	2008-02-05	2005-03-15	2005-03-17	ENSG00000165124	ENSG00000165124			15985	protein-coding gene	gene with protein product		611691	"""chromosome 9 open reading frame 13"""	C9orf13			Standard	NM_153366		Approved	bA427L11.3, POLYDOM, FLJ13529	uc010mtz.3	Q4LDE5	OTTHUMG00000020482	ENST00000401783.2:c.5429A>C	9.37:g.113192655T>G	ENSP00000384917:p.Glu1810Ala	Somatic	193	0	0		WXS	Illumina HiSeq	Phase_I	174	4	0.0229885	NM_153366	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Missense_Mutation	SNP	ENST00000401783.2	37	CCDS48004.1	495	0.22664835164835165	10	0.02032520325203252	84	0.23204419889502761	249	0.4353146853146853	152	0.20052770448548812	T	6.654	0.489110	0.12641	0.036494	0.169985	ENSG00000165124	ENST00000401783;ENST00000374469	T;T	0.64991	-0.13;-0.13	5.27	2.82	0.32997	Complement control module (2);Sushi/SCR/CCP (3);	0.403453	0.29021	N	0.013385	T	0.00012	0.0000	L	0.37897	1.145	0.21915	P	0.99947619	B	0.11235	0.004	B	0.12156	0.007	T	0.41538	-0.9503	9	0.10636	T	0.68	.	8.6135	0.33817	0.1283:0.0:0.1345:0.7371	rs2986671;rs3739449;rs11567627;rs17807596;rs2986671	1810	Q4LDE5	SVEP1_HUMAN	A	1810;1787	ENSP00000384917:E1810A;ENSP00000363593:E1787A	ENSP00000363593:E1787A	E	-	2	0	SVEP1	112232476	0.493000	0.26035	0.022000	0.16811	0.798000	0.45092	2.345000	0.44018	0.397000	0.25310	0.533000	0.62120	GAA	T|0.723;G|0.277	0.277	strong		0.408	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
KANSL3	55683	hgsc.bcm.edu	37	2	97271090	97271090	+	Missense_Mutation	SNP	G	G	A	rs35715176	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr2:97271090G>A	ENST00000431828.1	-	15	1976	c.1900C>T	c.(1900-1902)Cct>Tct	p.P634S	KANSL3_ENST00000440133.1_Missense_Mutation_p.P454S|KANSL3_ENST00000487070.1_5'UTR|KANSL3_ENST00000599854.1_Missense_Mutation_p.P547S|KANSL3_ENST00000441706.2_Intron			Q9P2N6	KANL3_HUMAN	KAT8 regulatory NSL complex subunit 3	660					chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)	histone acetyltransferase complex (GO:0000123)|intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)											GGAGCACAAGGCCCTCCAGCT	0.537													G|||	216	0.043131	0.0008	0.013	5008	,	,		21220	0.1438		0.0249	False		,,,				2504	0.0368				p.P634S		Atlas-SNP	.											.	.	.	.	0			c.C1900T						PASS	.	G	SER/PRO,SER/PRO	19,3929		0,19,1955	81.0	82.0	81.0		1900,1639	2.6	0.0	2	dbSNP_126	81	128,8174		1,126,4024	yes	missense,missense	KIAA1310	NM_001115016.1,NM_017991.4	74,74	1,145,5979	AA,AG,GG		1.5418,0.4813,1.2	benign,benign	634/879,547/792	97271090	147,12103	1974	4151	6125	SO:0001583	missense	55683	exon15			CACAAGGCCCTCC	BC063792	CCDS46361.1	2q11.2	2011-10-31	2011-10-31	2011-10-31	ENSG00000114982	ENSG00000114982			25473	protein-coding gene	gene with protein product			"""KIAA1310"""	KIAA1310			Standard	NM_001115016		Approved	FLJ10081, Rcd1, NSL3	uc002swn.5	Q9P2N6	OTTHUMG00000155249	ENST00000431828.1:c.1900C>T	2.37:g.97271090G>A	ENSP00000396749:p.Pro634Ser	Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	173	7	0.0404624	NM_001115016	A1L184|D3DXH3|D3DXH4|Q05BU4|Q6P3X2|Q6PJH6|Q86T19|Q96L64|Q9H0C9|Q9H8C9|Q9HAP8|Q9NWE5	Missense_Mutation	SNP	ENST00000431828.1	37	CCDS46361.1	132	0.06043956043956044	1	0.0020325203252032522	6	0.016574585635359115	107	0.18706293706293706	18	0.023746701846965697	G	9.096	1.002849	0.19121	0.004813	0.015418	ENSG00000114982	ENST00000354204;ENST00000447759;ENST00000431828;ENST00000440133;ENST00000444759	T;T	0.40476	1.03;1.05	5.42	2.62	0.31277	.	0.617048	0.17418	N	0.174938	T	0.00039	0.0001	N	0.04508	-0.205	0.54753	P	1.399999999995849E-5	B;B;B;B	0.06786	0.0;0.001;0.001;0.001	B;B;B;B	0.06405	0.0;0.001;0.001;0.002	T	0.25433	-1.0132	9	0.08179	T	0.78	.	5.0282	0.14396	0.1843:0.1741:0.6416:0.0	rs35715176	428;634;547;522	B4E1W4;Q9P2N6-3;Q9P2N6-5;Q9P2N6-6	.;.;.;.	S	547;522;634;454;428	ENSP00000396749:P634S;ENSP00000406207:P454S	ENSP00000346144:P547S	P	-	1	0	KIAA1310	96634817	0.052000	0.20516	0.033000	0.17914	0.996000	0.88848	0.518000	0.22847	0.658000	0.30925	0.655000	0.94253	CCT	G|0.949;A|0.051	0.051	strong		0.537	KANSL3-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339040.2	NM_017991	
ENDOD1	23052	hgsc.bcm.edu	37	11	94862577	94862577	+	Missense_Mutation	SNP	G	G	T	rs3740861	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr11:94862577G>T	ENST00000278505.4	+	2	1455	c.1337G>T	c.(1336-1338)gGc>gTc	p.G446V		NM_015036.2	NP_055851.1	O94919	ENDD1_HUMAN	endonuclease domain containing 1	446			G -> V (in dbSNP:rs3740861).			extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			breast(1)|endometrium(2)|large_intestine(3)|lung(4)|upper_aerodigestive_tract(1)	11		Acute lymphoblastic leukemia(157;2.33e-05)|all_hematologic(158;0.00824)				TACACCATGGGCGCTATTCCA	0.532													G|||	1002	0.20008	0.087	0.196	5008	,	,		19140	0.122		0.2684	False		,,,				2504	0.3661				p.G446V		Atlas-SNP	.											ENDOD1,NS,carcinoma,-1,1	ENDOD1	26	1	0			c.G1337T						scavenged	.	G	VAL/GLY	488,3592		31,426,1583	189.0	180.0	183.0		1337	6.0	0.1	11	dbSNP_107	183	2329,6089		319,1691,2199	yes	missense	ENDOD1	NM_015036.2	109	350,2117,3782	TT,TG,GG		27.6669,11.9608,22.5396	probably-damaging	446/501	94862577	2817,9681	2040	4209	6249	SO:0001583	missense	23052	exon2			CCATGGGCGCTAT	BC026191	CCDS41699.1	11q21	2010-03-19			ENSG00000149218	ENSG00000149218			29129	protein-coding gene	gene with protein product						10048485	Standard	NM_015036		Approved	KIAA0830	uc001pfh.3	O94919	OTTHUMG00000167835	ENST00000278505.4:c.1337G>T	11.37:g.94862577G>T	ENSP00000278505:p.Gly446Val	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	204	8	0.0392157	NM_015036	A8K6K8|Q6GQY5|Q8TAQ8	Missense_Mutation	SNP	ENST00000278505.4	37	CCDS41699.1	392	0.1794871794871795	53	0.10772357723577236	68	0.1878453038674033	66	0.11538461538461539	205	0.2704485488126649	G	13.52	2.261585	0.39995	0.119608	0.276669	ENSG00000149218	ENST00000278505	T	0.36699	1.24	5.97	5.97	0.96955	.	0.532850	0.21869	N	0.067907	T	0.00012	0.0000	M	0.65975	2.015	0.36868	P	0.11124599999999996	D	0.65815	0.995	P	0.58172	0.834	T	0.00163	-1.1969	9	0.46703	T	0.11	-10.5144	20.4301	0.99081	0.0:0.0:1.0:0.0	rs3740861;rs17693261;rs52803898;rs58207096;rs3740861	446	O94919	ENDD1_HUMAN	V	446	ENSP00000278505:G446V	ENSP00000278505:G446V	G	+	2	0	ENDOD1	94502225	0.981000	0.34729	0.067000	0.19924	0.018000	0.09664	6.268000	0.72552	2.834000	0.97654	0.557000	0.71058	GGC	G|0.794;T|0.206	0.206	strong		0.532	ENDOD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396545.1	NM_015036	
ZNF276	92822	hgsc.bcm.edu	37	16	89789898	89789898	+	Missense_Mutation	SNP	T	T	C	rs6500437	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr16:89789898T>C	ENST00000443381.2	+	4	884	c.787T>C	c.(787-789)Tgg>Cgg	p.W263R	VPS9D1_ENST00000389386.3_5'Flank|ZNF276_ENST00000568064.1_Silent_p.H181H|ZNF276_ENST00000446326.2_Silent_p.H59H|ZNF276_ENST00000289816.5_Missense_Mutation_p.W188R	NM_001113525.1	NP_001106997.1	Q8N554	ZN276_HUMAN	zinc finger protein 276	263			W -> R (in dbSNP:rs6500437). {ECO:0000269|PubMed:14605947, ECO:0000269|PubMed:15489334}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(6)|prostate(1)	14		Lung NSC(15;2.19e-05)|all_lung(18;3.07e-05)|all_hematologic(23;0.0256)		BRCA - Breast invasive adenocarcinoma(80;0.0278)		CAAGTGGCCATGGGACAAAGA	0.657													T|||	2722	0.54353	0.5809	0.5562	5008	,	,		18600	0.7282		0.3101	False		,,,				2504	0.5337				p.W263R		Atlas-SNP	.											ZNF276_ENST00000443381,colon,carcinoma,0,2	ZNF276	70	2	0			c.T787C						scavenged	.	T	ARG/TRP,ARG/TRP	2271,2125	566.4+/-381.9	579,1113,506	39.0	34.0	36.0		787,562	3.1	1.0	16	dbSNP_116	36	2516,6074	387.0+/-342.0	381,1754,2160	yes	missense,missense	ZNF276	NM_001113525.1,NM_152287.3	101,101	960,2867,2666	CC,CT,TT		29.2899,48.3394,36.8628	benign,benign	263/615,188/540	89789898	4787,8199	2198	4295	6493	SO:0001583	missense	92822	exon4			TGGCCATGGGACA	AK026482	CCDS10986.1, CCDS45554.1	16q24.3	2014-02-17	2006-02-10	2006-02-10	ENSG00000158805	ENSG00000158805		"""Zinc fingers, C2H2-type"""	23330	protein-coding gene	gene with protein product	"""centromere protein Z"", ""zinc finger, AD-type"""	608460	"""zinc finger protein 276 homolog (mouse)"""	ZFP276		10936049, 20813266	Standard	NM_152287		Approved	MGC45417, ZNF477, CENPZ, CENP-Z, ZADT	uc002fos.4	Q8N554	OTTHUMG00000138050	ENST00000443381.2:c.787T>C	16.37:g.89789898T>C	ENSP00000415836:p.Trp263Arg	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	156	5	0.0320513	NM_001113525	Q0VGA1|Q2TBE8|Q3B7H7	Missense_Mutation	SNP	ENST00000443381.2	37	CCDS45554.1	1147	0.5251831501831502	283	0.5752032520325203	177	0.4889502762430939	450	0.7867132867132867	237	0.31266490765171506	T	14.51	2.558270	0.45590	0.516606	0.292899	ENSG00000158805	ENST00000289816;ENST00000443381	T;T	0.05447	3.44;3.48	5.42	3.13	0.36017	.	0.297893	0.33591	N	0.004757	T	0.00012	0.0000	L	0.45581	1.43	0.09310	P	1.0	B;B	0.16166	0.005;0.016	B;B	0.12837	0.008;0.008	T	0.31024	-0.9958	9	0.07644	T	0.81	-19.3524	6.2916	0.21063	0.1425:0.077:0.0:0.7805	rs6500437;rs58773785;rs6500437	101;263	B4DIT3;Q8N554	.;ZN276_HUMAN	R	188;263	ENSP00000289816:W188R;ENSP00000415836:W263R	ENSP00000289816:W188R	W	+	1	0	ZNF276	88317399	0.916000	0.31088	0.961000	0.40146	0.673000	0.39480	1.332000	0.33805	0.861000	0.35504	0.459000	0.35465	TGG	T|0.562;C|0.438	0.438	strong		0.657	ZNF276-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422517.1	NM_152287	
TMEM232	642987	hgsc.bcm.edu	37	5	109973902	109973902	+	Silent	SNP	T	T	G	rs1422495	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr5:109973902T>G	ENST00000455884.2	-	5	548	c.498A>C	c.(496-498)gcA>gcC	p.A166A	TMEM232_ENST00000515518.2_5'UTR|TMEM232_ENST00000429839.2_Silent_p.A166A			C9JQI7	TM232_HUMAN	transmembrane protein 232	166						integral component of membrane (GO:0016021)				breast(1)|kidney(2)	3						AACATACCTTTGCTAGCTTTA	0.303													T|||	434	0.0866613	0.0756	0.1153	5008	,	,		14761	0.0903		0.0895	False		,,,				2504	0.0746				p.A166A		Atlas-SNP	.											.	TMEM232	57	.	0			c.A498C						PASS	.	T		109,1275		3,103,586	76.0	63.0	67.0		498	0.9	0.3	5	dbSNP_88	67	276,2906		14,248,1329	no	coding-synonymous	TMEM232	NM_001039763.3		17,351,1915	GG,GT,TT		8.6738,7.8757,8.4319		166/658	109973902	385,4181	692	1591	2283	SO:0001819	synonymous_variant	642987	exon5			TACCTTTGCTAGC	AK125070	CCDS47253.1, CCDS47253.2	5q22.1	2014-02-12	2009-10-02		ENSG00000186952	ENSG00000186952			37270	protein-coding gene	gene with protein product							Standard	NM_001039763		Approved	FLJ43080	uc011cvh.2	C9JQI7	OTTHUMG00000163297	ENST00000455884.2:c.498A>C	5.37:g.109973902T>G		Somatic	303	0	0		WXS	Illumina HiSeq	Phase_I	245	10	0.0408163	NM_001039763	B4DKF4	Silent	SNP	ENST00000455884.2	37	CCDS47253.2																																																																																			T|0.910;G|0.090	0.090	strong		0.303	TMEM232-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372488.2	NM_001039763	
CADPS	8618	hgsc.bcm.edu	37	3	62647994	62647994	+	Missense_Mutation	SNP	C	C	A			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr3:62647994C>A	ENST00000383710.4	-	4	1313	c.964G>T	c.(964-966)Gcc>Tcc	p.A322S	CADPS_ENST00000357948.3_Missense_Mutation_p.A322S|CADPS_ENST00000283269.9_Missense_Mutation_p.A322S|CADPS_ENST00000490353.2_Missense_Mutation_p.A322S	NM_003716.3	NP_003707.2	Q9ULU8	CAPS1_HUMAN	Ca++-dependent secretion activator	322					catecholamine secretion (GO:0050432)|exocytosis (GO:0006887)|protein transport (GO:0015031)|synaptic vesicle priming (GO:0016082)|vesicle organization (GO:0016050)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|membrane (GO:0016020)|synapse (GO:0045202)	lipid binding (GO:0008289)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)			breast(3)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(24)|lung(38)|ovary(4)|prostate(3)|skin(3)|stomach(1)|urinary_tract(2)	92		Lung SC(41;0.0452)		BRCA - Breast invasive adenocarcinoma(55;5.98e-05)|KIRC - Kidney renal clear cell carcinoma(15;0.0246)|Kidney(15;0.0334)		CTTACCCTGGCTATTTGGTCT	0.488																																					p.A322S		Atlas-SNP	.											.	CADPS	387	.	0			c.G964T						PASS	.						174.0	149.0	158.0					3																	62647994		2203	4300	6503	SO:0001583	missense	8618	exon4			CCCTGGCTATTTG	U36448	CCDS2898.1, CCDS2899.1, CCDS46858.1	3p21.1	2013-01-10	2008-08-28		ENSG00000163618	ENSG00000163618		"""Pleckstrin homology (PH) domain containing"""	1426	protein-coding gene	gene with protein product		604667				1516133	Standard	NM_183393		Approved	CAPS, KIAA1121, CAPS1	uc003dll.2	Q9ULU8	OTTHUMG00000158651	ENST00000383710.4:c.964G>T	3.37:g.62647994C>A	ENSP00000373215:p.Ala322Ser	Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	36	18	0.5	NM_003716	A6NF60|Q13339|Q6GQQ6|Q8N2Z5|Q8N3M7|Q8NFR0|Q96BC2	Missense_Mutation	SNP	ENST00000383710.4	37	CCDS46858.1	.	.	.	.	.	.	.	.	.	.	C	15.88	2.965064	0.53507	.	.	ENSG00000163618	ENST00000383709;ENST00000383710;ENST00000357948;ENST00000283269;ENST00000490353	D;D;D;D	0.85088	-1.94;-1.94;-1.94;-1.94	5.54	5.54	0.83059	.	0.111048	0.64402	D	0.000006	D	0.86389	0.5921	N	0.20845	0.615	0.58432	D	0.999993	B;D;P	0.61697	0.073;0.99;0.657	B;D;B	0.73380	0.074;0.98;0.138	D	0.83718	0.0191	10	0.21014	T	0.42	.	18.2515	0.90005	0.0:1.0:0.0:0.0	.	322;322;322	Q9ULU8-2;Q9ULU8-3;Q9ULU8	.;.;CAPS1_HUMAN	S	322	ENSP00000373215:A322S;ENSP00000350632:A322S;ENSP00000283269:A322S;ENSP00000418736:A322S	ENSP00000283269:A322S	A	-	1	0	CADPS	62623034	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	5.387000	0.66243	2.606000	0.88127	0.655000	0.94253	GCC	.	.	none		0.488	CADPS-013	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351951.5	NM_003716, NM_183393, NM_183394	
SIPA1L2	57568	hgsc.bcm.edu	37	1	232539219	232539219	+	Missense_Mutation	SNP	C	C	T	rs2275303	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr1:232539219C>T	ENST00000366630.1	-	20	5273	c.4915G>A	c.(4915-4917)Ggc>Agc	p.G1639S	SIPA1L2_ENST00000262861.4_Missense_Mutation_p.G1639S|SIPA1L2_ENST00000308942.4_Missense_Mutation_p.G695S			Q9P2F8	SI1L2_HUMAN	signal-induced proliferation-associated 1 like 2	1639			G -> S (in dbSNP:rs2275303).		regulation of small GTPase mediated signal transduction (GO:0051056)		GTPase activator activity (GO:0005096)			NS(1)|breast(5)|central_nervous_system(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(49)|ovary(2)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	103		all_cancers(173;0.00605)|Prostate(94;0.128)|all_epithelial(177;0.186)				AACTCTTTGCCACTGCCTGGA	0.562													C|||	617	0.123203	0.0	0.072	5008	,	,		17239	0.4593		0.0089	False		,,,				2504	0.0971				p.G1639S		Atlas-SNP	.											.	SIPA1L2	218	.	0			c.G4915A						PASS	.	C	SER/GLY	18,3958		0,18,1970	90.0	101.0	98.0		4915	2.1	0.2	1	dbSNP_100	98	52,8272		0,52,4110	yes	missense	SIPA1L2	NM_020808.3	56	0,70,6080	TT,TC,CC		0.6247,0.4527,0.5691	possibly-damaging	1639/1723	232539219	70,12230	1988	4162	6150	SO:0001583	missense	57568	exon19			CTTTGCCACTGCC	AB037810	CCDS41474.1	1q42.2	2008-02-05			ENSG00000116991	ENSG00000116991			23800	protein-coding gene	gene with protein product		611609					Standard	NM_020808		Approved	KIAA1389	uc001hvg.3	Q9P2F8	OTTHUMG00000037820	ENST00000366630.1:c.4915G>A	1.37:g.232539219C>T	ENSP00000355589:p.Gly1639Ser	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	42	4	0.0952381	NM_020808	Q2TV88|Q5VXR7|Q5VXR8|Q641Q4|Q8NA38|Q96DZ3|Q9H9F6	Missense_Mutation	SNP	ENST00000366630.1	37	CCDS41474.1	304	0.1391941391941392	0	0.0	23	0.06353591160220995	272	0.4755244755244755	9	0.011873350923482849	C	8.696	0.908662	0.17833	0.004527	0.006247	ENSG00000116991	ENST00000366630;ENST00000262861;ENST00000308942	T;T;T	0.29397	1.57;1.57;1.57	4.94	2.09	0.27110	.	0.953922	0.08825	N	0.888251	T	0.00012	0.0000	L	0.43152	1.355	0.31410	P	0.675603	B;B	0.23735	0.09;0.001	B;B	0.28385	0.089;0.002	T	0.47100	-0.9143	9	0.30078	T	0.28	-7.8586	10.1777	0.42948	0.0:0.7843:0.0:0.2157	rs2275303;rs52800362;rs2275303	1639;695	Q9P2F8;Q9P2F8-2	SI1L2_HUMAN;.	S	1639;1639;695	ENSP00000355589:G1639S;ENSP00000262861:G1639S;ENSP00000309102:G695S	ENSP00000262861:G1639S	G	-	1	0	SIPA1L2	230605842	0.993000	0.37304	0.186000	0.23195	0.689000	0.40095	1.823000	0.39062	0.309000	0.22966	-0.149000	0.13747	GGC	C|0.855;T|0.145	0.145	strong		0.562	SIPA1L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092318.1	XM_045839	
KLHL6	89857	hgsc.bcm.edu	37	3	183209942	183209942	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr3:183209942C>T	ENST00000341319.3	-	7	1674	c.1639G>A	c.(1639-1641)Gag>Aag	p.E547K		NM_130446.2	NP_569713.2	Q8WZ60	KLHL6_HUMAN	kelch-like family member 6	547					B cell receptor signaling pathway (GO:0050853)|germinal center formation (GO:0002467)					breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(7)|kidney(1)|large_intestine(6)|liver(1)|lung(16)|ovary(2)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	44	all_cancers(143;9.2e-12)|Ovarian(172;0.0172)		all cancers(12;1.29e-44)|Epithelial(37;1.24e-38)|LUSC - Lung squamous cell carcinoma(7;2.58e-24)|Lung(8;1.79e-22)|OV - Ovarian serous cystadenocarcinoma(80;2.32e-22)			CTGGCCCGCTCGTGGCTGAGC	0.657																																					p.E547K		Atlas-SNP	.											.	KLHL6	100	.	0			c.G1639A						PASS	.						39.0	39.0	39.0					3																	183209942		2202	4299	6501	SO:0001583	missense	89857	exon7			CCCGCTCGTGGCT	AF441792	CCDS3245.2	3q27.3	2013-01-30	2013-01-30		ENSG00000172578	ENSG00000172578		"""Kelch-like"", ""BTB/POZ domain containing"""	18653	protein-coding gene	gene with protein product	"""kelch-like protein KLHL6"""	614214	"""kelch-like 6 (Drosophila)"""			11214971, 12617994	Standard	NM_130446		Approved	FLJ00029	uc003flr.3	Q8WZ60	OTTHUMG00000148673	ENST00000341319.3:c.1639G>A	3.37:g.183209942C>T	ENSP00000341342:p.Glu547Lys	Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	151	52	0.344371	NM_130446	B2RB31|D3DNS8|Q8N5I1|Q8N892	Missense_Mutation	SNP	ENST00000341319.3	37	CCDS3245.2	.	.	.	.	.	.	.	.	.	.	C	12.27	1.888221	0.33348	.	.	ENSG00000172578	ENST00000341319	T	0.65732	-0.17	5.8	5.8	0.92144	Kelch-type beta propeller (1);	0.000000	0.85682	D	0.000000	T	0.48295	0.1492	N	0.21194	0.64	0.53688	D	0.999972	P	0.37663	0.604	B	0.37508	0.252	T	0.48364	-0.9042	10	0.02654	T	1	.	20.029	0.97531	0.0:1.0:0.0:0.0	.	547	Q8WZ60	KLHL6_HUMAN	K	547	ENSP00000341342:E547K	ENSP00000341342:E547K	E	-	1	0	KLHL6	184692636	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.907000	0.69908	2.742000	0.94016	0.591000	0.81541	GAG	.	.	none		0.657	KLHL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309024.1	NM_130446	
DNAH9	1770	hgsc.bcm.edu	37	17	11648332	11648332	+	Silent	SNP	C	C	T	rs3744578	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr17:11648332C>T	ENST00000262442.4	+	31	6398	c.6330C>T	c.(6328-6330)aaC>aaT	p.N2110N	DNAH9_ENST00000454412.2_Silent_p.N2110N	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	2110					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)		GAGACCCCAACTTCGAAGCTT	0.532													C|||	3857	0.770168	0.5605	0.8386	5008	,	,		19040	0.9345		0.7932	False		,,,				2504	0.8119				p.N2110N		Atlas-SNP	.											.	DNAH9	695	.	0			c.C6330T						PASS	.	C		2698,1708	651.5+/-399.2	832,1034,337	95.0	98.0	97.0		6330	3.4	0.4	17	dbSNP_107	97	6873,1727	736.3+/-407.0	2731,1411,158	no	coding-synonymous	DNAH9	NM_001372.3		3563,2445,495	TT,TC,CC		20.0814,38.7653,26.4109		2110/4487	11648332	9571,3435	2203	4300	6503	SO:0001819	synonymous_variant	1770	exon31			CCCCAACTTCGAA	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.6330C>T	17.37:g.11648332C>T		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	123	5	0.0406504	NM_001372	A2VCQ8|O15064|O95494|Q9NQ28	Silent	SNP	ENST00000262442.4	37	CCDS11160.1																																																																																			C|0.256;T|0.744	0.744	strong		0.532	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372	
ERCC6	2074	hgsc.bcm.edu	37	10	50678317	50678317	+	Missense_Mutation	SNP	C	C	G	rs4253211	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr10:50678317C>G	ENST00000355832.5	-	18	3767	c.3689G>C	c.(3688-3690)cGt>cCt	p.R1230P	ERCC6_ENST00000542458.1_Missense_Mutation_p.R600P|RP11-123B3.2_ENST00000423283.1_RNA|ERCC6_ENST00000465653.1_5'UTR	NM_000124.2	NP_000115.1	Q03468	ERCC6_HUMAN	excision repair cross-complementation group 6	1230			R -> P (in dbSNP:rs4253211). {ECO:0000269|Ref.3}.		activation of JNKK activity (GO:0007256)|activation of JUN kinase activity (GO:0007257)|ATP catabolic process (GO:0006200)|base-excision repair (GO:0006284)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|multicellular organism growth (GO:0035264)|nucleotide-excision repair (GO:0006289)|photoreceptor cell maintenance (GO:0045494)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|positive regulation of protein tyrosine kinase activity (GO:0061098)|pyrimidine dimer repair (GO:0006290)|regulation of DNA-templated transcription, elongation (GO:0032784)|response to gamma radiation (GO:0010332)|response to oxidative stress (GO:0006979)|response to superoxide (GO:0000303)|response to toxic substance (GO:0009636)|response to UV (GO:0009411)|response to UV-B (GO:0010224)|response to X-ray (GO:0010165)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase II promoter (GO:0006366)|transcription-coupled nucleotide-excision repair (GO:0006283)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)|protein N-terminus binding (GO:0047485)|protein tyrosine kinase activator activity (GO:0030296)	p.R1230P(1)		breast(5)|central_nervous_system(1)|endometrium(6)|kidney(5)|large_intestine(15)|lung(19)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	64						CTTCTGGTAACGCCTTTTCTT	0.413								Direct reversal of damage;Nucleotide excision repair (NER)					C|||	238	0.047524	0.0076	0.0274	5008	,	,		20047	0.0804		0.0915	False		,,,				2504	0.0368				p.K1230T		Atlas-SNP	.											ERCC6,NS,carcinoma,0,1	ERCC6	162	1	1	Substitution - Missense(1)	stomach(1)	c.A3689C						scavenged	.	C	PRO/ARG	92,4314	76.8+/-115.0	0,92,2111	368.0	347.0	354.0		3689	-7.1	0.0	10	dbSNP_111	354	827,7773	191.3+/-237.5	46,735,3519	yes	missense	ERCC6	NM_000124.2	103	46,827,5630	GG,GC,CC		9.6163,2.0881,7.066	benign	1230/1494	50678317	919,12087	2203	4300	6503	SO:0001583	missense	2074	exon18			TGGTAACGCCTTT	L04791	CCDS7229.1	10q11	2014-09-17	2014-03-07		ENSG00000225830	ENSG00000225830			3438	protein-coding gene	gene with protein product	"""Cockayne syndrome B protein"""	609413	"""excision repair cross-complementing rodent repair deficiency, complementation group 6"""	CKN2		1339317, 19179336	Standard	NM_000124		Approved	CSB, RAD26, ARMD5	uc001jhs.5	Q03468	OTTHUMG00000018195	ENST00000355832.5:c.3689G>C	10.37:g.50678317C>G	ENSP00000348089:p.Arg1230Pro	Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	162	5	0.0308642	NM_000124	D3DX94|Q5W0L9	Missense_Mutation	SNP	ENST00000355832.5	37	CCDS7229.1	140	0.0641025641025641	5	0.01016260162601626	11	0.03038674033149171	58	0.10139860139860139	66	0.0870712401055409	C	9.193	1.026462	0.19512	0.020881	0.096163	ENSG00000225830	ENST00000355832;ENST00000374129;ENST00000542458	D;T	0.83419	-1.72;-1.46	5.41	-7.13	0.01532	.	.	.	.	.	T	0.07007	0.0178	M	0.62016	1.91	0.58432	P	1.0000000000287557E-6	B;B	0.06786	0.001;0.001	B;B	0.08055	0.002;0.003	T	0.37033	-0.9723	8	0.35671	T	0.21	-2.4611	5.033	0.14419	0.0753:0.6027:0.1507:0.1713	rs4253211;rs17783841;rs52816732;rs56589667;rs4253211	1230;607	Q03468;Q59FF6	ERCC6_HUMAN;.	P	1230;607;600	ENSP00000348089:R1230P;ENSP00000445134:R600P	ENSP00000348089:R1230P	R	-	2	0	ERCC6	50348323	0.000000	0.05858	0.004000	0.12327	0.601000	0.36947	-0.548000	0.06048	-1.579000	0.01646	-0.229000	0.12294	CGT	C|0.930;G|0.070	0.070	strong		0.413	ERCC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047990.1	NM_000124	
PRRC2A	7916	hgsc.bcm.edu	37	6	31602967	31602967	+	Missense_Mutation	SNP	G	G	A	rs1046089	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr6:31602967G>A	ENST00000376033.2	+	22	5453	c.5219G>A	c.(5218-5220)cGt>cAt	p.R1740H	PRRC2A_ENST00000376007.4_Missense_Mutation_p.R1740H	NM_004638.3	NP_004629.3	P48634	PRC2A_HUMAN	proline-rich coiled-coil 2A	1740	4 X 57 AA type A repeats.		R -> H (in dbSNP:rs1046089). {ECO:0000269|PubMed:14574404, ECO:0000269|PubMed:14656967, ECO:0000269|Ref.6}.			cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(6)|central_nervous_system(1)|endometrium(7)|kidney(5)|large_intestine(14)|lung(19)|ovary(3)|pancreas(2)|prostate(4)|skin(5)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	70						CGATCACAGCGTACAGACCGA	0.622													G|||	1954	0.390176	0.5431	0.3646	5008	,	,		17959	0.3512		0.3449	False		,,,				2504	0.2883				p.R1740H		Atlas-SNP	.											.	PRRC2A	152	.	0			c.G5219A	GRCh37	CM090830	PRRC2A	M	rs1046089	PASS	.	G	HIS/ARG,HIS/ARG	2245,2161	594.2+/-388.2	578,1089,536	85.0	82.0	83.0	http://www.ncbi.nlm.nih.gov/pubmed?term	5219,5219	5.5	1.0	6	dbSNP_86	83	2971,5629	460.2+/-365.1	516,1939,1845	yes	missense,missense	PRRC2A	NM_004638.3,NM_080686.2	29,29	1094,3028,2381	AA,AG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	34.5465,49.0468,40.1046	probably-damaging,probably-damaging	1740/2158,1740/2158	31602967	5216,7790	2203	4300	6503	SO:0001583	missense	7916	exon22			CACAGCGTACAGA	M31293	CCDS4708.1	6p21.3	2010-12-09	2010-12-09	2010-12-09	ENSG00000204469	ENSG00000204469			13918	protein-coding gene	gene with protein product		142580	"""HLA-B associated transcript 2"""	BAT2		2156268, 8499947	Standard	NM_080686		Approved	G2, D6S51E	uc003nvc.4	P48634	OTTHUMG00000031168	ENST00000376033.2:c.5219G>A	6.37:g.31602967G>A	ENSP00000365201:p.Arg1740His	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	64	4	0.0625	NM_004638	B0UX77|B0UZE9|B0UZL3|O95875|Q05BK4|Q4LE37|Q5SQ29|Q5SQ30|Q5ST84|Q5STX6|Q5STX7|Q68DW9|Q6P9P7|Q6PIN1|Q8MGQ9|Q96QC6	Missense_Mutation	SNP	ENST00000376033.2	37	CCDS4708.1	862	0.3946886446886447	262	0.532520325203252	127	0.35082872928176795	202	0.3531468531468531	271	0.3575197889182058	G	15.40	2.822060	0.50739	0.509532	0.345465	ENSG00000204469	ENST00000424184;ENST00000435052;ENST00000376007;ENST00000376033;ENST00000376010	T;T	0.01745	4.66;4.66	5.51	5.51	0.81932	.	0.218848	0.33075	N	0.005319	T	0.01592	0.0051	L	0.36672	1.1	0.27289	P	0.9578908	D	0.52996	0.957	P	0.46339	0.513	T	0.60131	-0.7323	9	0.87932	D	0	0.17	16.4508	0.83990	0.0:0.0:1.0:0.0	rs1046089;rs6913649;rs17207246;rs17845914;rs17857495;rs17858890;rs59917316;rs1046089	1740	P48634	PRC2A_HUMAN	H	1734;1723;1740;1740;965	ENSP00000365175:R1740H;ENSP00000365201:R1740H	ENSP00000365175:R1740H	R	+	2	0	PRRC2A	31710946	0.999000	0.42202	0.983000	0.44433	0.993000	0.82548	3.354000	0.52254	2.873000	0.98535	0.561000	0.74099	CGT	G|0.611;A|0.389	0.389	strong		0.622	PRRC2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259319.1	NM_080686	
OR1S2	219958	hgsc.bcm.edu	37	11	57971203	57971203	+	Missense_Mutation	SNP	C	C	G			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr11:57971203C>G	ENST00000302592.6	-	1	450	c.451G>C	c.(451-453)Gcc>Ccc	p.A151P		NM_001004459.1	NP_001004459.1	Q8NGQ3	OR1S2_HUMAN	olfactory receptor, family 1, subfamily S, member 2	151						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(11)|kidney(1)|large_intestine(4)|lung(23)|ovary(2)|skin(2)|stomach(2)|urinary_tract(1)	46		Breast(21;0.0589)				CCGAACCTGGCCCGCATGAAA	0.473																																					p.A151P		Atlas-SNP	.											OR1S2,NS,carcinoma,0,3	OR1S2	119	3	0			c.G451C						scavenged	.						163.0	154.0	157.0					11																	57971203		2201	4296	6497	SO:0001583	missense	219958	exon1			ACCTGGCCCGCAT	BK004297	CCDS31545.1	11q12.1	2012-08-09			ENSG00000197887	ENSG00000197887		"""GPCR / Class A : Olfactory receptors"""	15141	protein-coding gene	gene with protein product							Standard	NM_001004459		Approved		uc010rkb.2	Q8NGQ3	OTTHUMG00000167541	ENST00000302592.6:c.451G>C	11.37:g.57971203C>G	ENSP00000305469:p.Ala151Pro	Somatic	148	1	0.00675676		WXS	Illumina HiSeq	Phase_I	183	5	0.0273224	NM_001004459	Q6IFG5|Q96R85	Missense_Mutation	SNP	ENST00000302592.6	37	CCDS31545.1	.	.	.	.	.	.	.	.	.	.	G	0	-2.753352	0.00085	.	.	ENSG00000197887	ENST00000302592	T	0.34275	1.37	4.47	-1.08	0.09936	GPCR, rhodopsin-like superfamily (1);	0.857144	0.09920	N	0.738596	T	0.04770	0.0129	N	0.00089	-2.185	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.30149	-0.9988	10	0.02654	T	1	.	0.1523	0.00094	0.2967:0.2321:0.2346:0.2366	.	151	Q8NGQ3	OR1S2_HUMAN	P	151	ENSP00000305469:A151P	ENSP00000305469:A151P	A	-	1	0	OR1S2	57727779	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.298000	0.02756	-0.572000	0.06006	-0.120000	0.15030	GCC	.	.	none		0.473	OR1S2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394703.2	NM_001004459	
FAM46C	54855	hgsc.bcm.edu	37	1	118166096	118166096	+	Silent	SNP	C	C	T	rs2884587	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr1:118166096C>T	ENST00000369448.3	+	2	853	c.606C>T	c.(604-606)atC>atT	p.I202I		NM_017709.3	NP_060179.2	Q5VWP2	FA46C_HUMAN	family with sequence similarity 46, member C	202										endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(1)|lung(7)|ovary(1)|upper_aerodigestive_tract(1)	15	Lung SC(450;0.225)	all_cancers(81;0.000101)|all_lung(203;3.4e-06)|all_epithelial(167;4.98e-06)|Lung NSC(69;2.33e-05)		Lung(183;0.0576)|LUSC - Lung squamous cell carcinoma(189;0.192)|Colorectal(144;0.247)		ATAATCCCATCTCTGAGCACT	0.483			"""Mis, F, O"""		MM					Multiple Myeloma(3;1.13e-06)			C|||	673	0.134385	0.0159	0.2233	5008	,	,		21188	0.1141		0.164	False		,,,				2504	0.2219				p.I202I		Atlas-SNP	.		Rec	yes		1	1p12	54855	"""family with sequence similarity 46, member C"""		L	.	FAM46C	25	.	0			c.C606T						PASS	.	C		211,4195	129.0+/-165.8	10,191,2002	137.0	132.0	134.0		606	1.5	0.9	1	dbSNP_101	134	1423,7177	273.5+/-290.7	121,1181,2998	no	coding-synonymous	FAM46C	NM_017709.3		131,1372,5000	TT,TC,CC		16.5465,4.7889,12.5634		202/392	118166096	1634,11372	2203	4300	6503	SO:0001819	synonymous_variant	54855	exon2			TCCCATCTCTGAG	BC036516	CCDS896.1	1p12	2008-02-05			ENSG00000183508	ENSG00000183508			24712	protein-coding gene	gene with protein product		613952				12477932	Standard	NM_017709		Approved	FLJ20202	uc001ehe.3	Q5VWP2	OTTHUMG00000013703	ENST00000369448.3:c.606C>T	1.37:g.118166096C>T		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	117	5	0.042735	NM_017709	A3KMG2|Q8NE25|Q9NXK0	Silent	SNP	ENST00000369448.3	37	CCDS896.1																																																																																			C|0.874;T|0.126	0.126	strong		0.483	FAM46C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038424.1	NM_017709	
DLGAP1	9229	hgsc.bcm.edu	37	18	3814275	3814275	+	Splice_Site	SNP	T	T	A			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr18:3814275T>A	ENST00000315677.3	-	5	1553		c.e5-2		DLGAP1_ENST00000400149.3_Splice_Site|DLGAP1_ENST00000400145.2_Splice_Site|DLGAP1_ENST00000400155.1_Splice_Site|DLGAP1_ENST00000581527.1_Splice_Site|snoU13_ENST00000459060.1_RNA|DLGAP1_ENST00000515196.2_Splice_Site|DLGAP1_ENST00000400147.2_Splice_Site|DLGAP1_ENST00000478161.1_Splice_Site|DLGAP1_ENST00000539435.1_Splice_Site|DLGAP1_ENST00000581699.1_Splice_Site|DLGAP1_ENST00000400150.3_Splice_Site|DLGAP1_ENST00000584874.1_Splice_Site|DLGAP1_ENST00000534970.1_Splice_Site	NM_004746.3	NP_004737.2	O14490	DLGP1_HUMAN	discs, large (Drosophila) homolog-associated protein 1						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)				TTGTGGAACCTATTCAGATAG	0.338																																					.		Atlas-SNP	.											.	DLGAP1	201	.	0			c.958-2A>T						PASS	.						87.0	84.0	85.0					18																	3814275		2203	4300	6503	SO:0001630	splice_region_variant	9229	exon6			GGAACCTATTCAG	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.958-2A>T	18.37:g.3814275T>A		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	95	23	0.242105	NM_004746	A8MWN8|B2RMU8|B7WPA1|B7Z2H2|B7Z2I2|B7Z9Y4|O14489|P78335	Splice_Site	SNP	ENST00000315677.3	37	CCDS11836.1	.	.	.	.	.	.	.	.	.	.	T	17.08	3.297901	0.60086	.	.	ENSG00000170579	ENST00000315677;ENST00000400147;ENST00000400150;ENST00000400149;ENST00000400155;ENST00000534970;ENST00000539435;ENST00000400145;ENST00000515196	.	.	.	5.85	5.85	0.93711	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.2416	0.82411	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	DLGAP1	3804275	1.000000	0.71417	0.959000	0.39883	0.990000	0.78478	7.942000	0.87708	2.229000	0.72834	0.533000	0.62120	.	.	.	none		0.338	DLGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254394.4		Intron
FAT1	2195	hgsc.bcm.edu	37	4	187542755	187542755	+	Missense_Mutation	SNP	T	T	C	rs28489116	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr4:187542755T>C	ENST00000441802.2	-	10	5194	c.4985A>G	c.(4984-4986)aAc>aGc	p.N1662S		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	1662	Cadherin 14. {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)	p.N1662S(2)|p.N1665S(1)		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						CGGAGAGGCGTTGTCAGCAAT	0.408										HNSCC(5;0.00058)			T|||	1004	0.200479	0.2141	0.1988	5008	,	,		19433	0.3849		0.1113	False		,,,				2504	0.0849				p.N1662S	Colon(197;1040 2055 4143 4984 49344)	Atlas-SNP	.											FAT1,NS,carcinoma,0,2	FAT1	500	2	3	Substitution - Missense(3)	prostate(3)	c.A4985G						PASS	.	T	SER/ASN	605,3161		61,483,1339	94.0	91.0	92.0		4985	5.2	1.0	4	dbSNP_125	92	971,7257		69,833,3212	yes	missense	FAT1	NM_005245.3	46	130,1316,4551	CC,CT,TT		11.8012,16.0648,13.1399	benign	1662/4589	187542755	1576,10418	1883	4114	5997	SO:0001583	missense	2195	exon10			GAGGCGTTGTCAG	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.4985A>G	4.37:g.187542755T>C	ENSP00000406229:p.Asn1662Ser	Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	150	7	0.0466667	NM_005245		Missense_Mutation	SNP	ENST00000441802.2	37	CCDS47177.1	495	0.22664835164835165	103	0.20934959349593496	75	0.20718232044198895	229	0.40034965034965037	88	0.11609498680738786	T	16.23	3.063325	0.55432	0.160648	0.118012	ENSG00000083857	ENST00000441802;ENST00000260147	T	0.60672	0.17	5.19	5.19	0.71726	Cadherin (3);Cadherin-like (1);	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	M	0.77616	2.38	0.09310	P	0.99999999775895	D	0.71674	0.998	D	0.79784	0.993	T	0.17379	-1.0371	9	0.37606	T	0.19	.	15.5098	0.75772	0.0:0.0:0.0:1.0	rs28489116;rs58264946	1662	Q14517	FAT1_HUMAN	S	1662;1664	ENSP00000406229:N1662S	ENSP00000260147:N1664S	N	-	2	0	FAT1	187779749	1.000000	0.71417	0.999000	0.59377	0.794000	0.44872	7.825000	0.86693	2.304000	0.77564	0.528000	0.53228	AAC	T|0.794;C|0.206	0.206	strong		0.408	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245	
CUBN	8029	hgsc.bcm.edu	37	10	16948390	16948390	+	Missense_Mutation	SNP	G	G	C	rs3740168	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr10:16948390G>C	ENST00000377833.4	-	50	7789	c.7724C>G	c.(7723-7725)cCa>cGa	p.P2575R		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	2575	CUB 19. {ECO:0000255|PROSITE- ProRule:PRU00059}.		P -> R (in dbSNP:rs3740168). {ECO:0000269|PubMed:10080186}.		cholesterol metabolic process (GO:0008203)|cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|tissue homeostasis (GO:0001894)|vitamin D metabolic process (GO:0042359)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|Golgi apparatus (GO:0005794)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|cobalamin binding (GO:0031419)|protein homodimerization activity (GO:0042803)|receptor activity (GO:0004872)|transporter activity (GO:0005215)			breast(8)|central_nervous_system(4)|cervix(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(42)|liver(1)|lung(107)|ovary(9)|pancreas(2)|prostate(3)|skin(9)|stomach(3)|upper_aerodigestive_tract(11)|urinary_tract(8)	241					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	AGGAGTATTTGGAAGAGACCC	0.428													G|||	338	0.067492	0.0045	0.0634	5008	,	,		18958	0.1369		0.0219	False		,,,				2504	0.1309				p.P2575R		Atlas-SNP	.											CUBN,right_upper_lobe,carcinoma,-1,1	CUBN	515	1	0			c.C7724G						scavenged	.	G	ARG/PRO	31,4375	37.6+/-69.7	0,31,2172	65.0	66.0	66.0		7724	4.6	0.0	10	dbSNP_107	66	127,8469	63.9+/-126.0	4,119,4175	yes	missense	CUBN	NM_001081.3	103	4,150,6347	CC,CG,GG		1.4774,0.7036,1.2152	benign	2575/3624	16948390	158,12844	2203	4298	6501	SO:0001583	missense	8029	exon50			GTATTTGGAAGAG	AF034611	CCDS7113.1	10p12	2014-09-17			ENSG00000107611	ENSG00000107611			2548	protein-coding gene	gene with protein product		602997		MGA1		9572993, 9478979	Standard	NM_001081		Approved	IFCR, gp280	uc001ioo.3	O60494	OTTHUMG00000017741	ENST00000377833.4:c.7724C>G	10.37:g.16948390G>C	ENSP00000367064:p.Pro2575Arg	Somatic	133	1	0.0075188		WXS	Illumina HiSeq	Phase_I	133	6	0.0451128	NM_001081	B0YIZ4|Q5VTA6|Q96RU9	Missense_Mutation	SNP	ENST00000377833.4	37	CCDS7113.1	125	0.05723443223443223	5	0.01016260162601626	23	0.06353591160220995	83	0.1451048951048951	14	0.018469656992084433	G	7.428	0.638180	0.14386	0.007036	0.014774	ENSG00000107611	ENST00000377833	T	0.17370	2.28	5.54	4.64	0.57946	CUB (5);	0.780797	0.11184	N	0.590670	T	0.00039	0.0001	N	0.02674	-0.535	0.45118	P	0.0018620000000000303	B	0.25904	0.137	B	0.28991	0.097	T	0.39231	-0.9624	9	0.14252	T	0.57	.	8.2189	0.31530	0.1009:0.0:0.746:0.1531	rs3740168	2575	O60494	CUBN_HUMAN	R	2575	ENSP00000367064:P2575R	ENSP00000367064:P2575R	P	-	2	0	CUBN	16988396	0.008000	0.16893	0.002000	0.10522	0.054000	0.15201	1.784000	0.38674	1.474000	0.48178	-0.245000	0.11935	CCA	G|0.974;C|0.026	0.026	strong		0.428	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081	
OR4D1	26689	hgsc.bcm.edu	37	17	56233034	56233034	+	Missense_Mutation	SNP	C	C	A	rs7218964	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr17:56233034C>A	ENST00000268912.5	+	1	541	c.520C>A	c.(520-522)Cta>Ata	p.L174I		NM_012374.1	NP_036506.1	Q15615	OR4D1_HUMAN	olfactory receptor, family 4, subfamily D, member 1	174			L -> I (in dbSNP:rs7218964). {ECO:0000269|PubMed:12213199, ECO:0000269|PubMed:9119360}.		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)	p.L174I(1)		kidney(2)|large_intestine(4)|lung(4)|ovary(1)|stomach(1)|urinary_tract(1)	13						CCCCAATATCCTAGATAACTT	0.542													C|||	1329	0.265375	0.4539	0.2378	5008	,	,		18842	0.1478		0.1809	False		,,,				2504	0.2382				p.L174I		Atlas-SNP	.											OR4D1,NS,carcinoma,0,1	OR4D1	48	1	1	Substitution - Missense(1)	stomach(1)	c.C520A						scavenged	.	C	ILE/LEU	1783,2623	526.0+/-371.8	365,1053,785	113.0	110.0	111.0		520	5.6	1.0	17	dbSNP_116	111	1627,6973	301.3+/-305.4	151,1325,2824	yes	missense	OR4D1	NM_012374.1	5	516,2378,3609	AA,AC,CC		18.9186,40.4675,26.2187	probably-damaging	174/311	56233034	3410,9596	2203	4300	6503	SO:0001583	missense	26689	exon1			AATATCCTAGATA	X89670	CCDS42365.1	17q22	2012-08-09			ENSG00000141194	ENSG00000141194		"""GPCR / Class A : Olfactory receptors"""	8293	protein-coding gene	gene with protein product				OR4D3		9119360	Standard	NM_012374		Approved	TPCR16	uc010wno.2	Q15615		ENST00000268912.5:c.520C>A	17.37:g.56233034C>A	ENSP00000365451:p.Leu174Ile	Somatic	98	1	0.0102041		WXS	Illumina HiSeq	Phase_I	86	4	0.0465116	NM_012374	B2RN14|Q8NGB1|Q96R76	Missense_Mutation	SNP	ENST00000268912.5	37	CCDS42365.1	508	0.2326007326007326	210	0.4268292682926829	72	0.19889502762430938	83	0.1451048951048951	143	0.18865435356200527	c	8.333	0.827031	0.16749	0.404675	0.189186	ENSG00000141194	ENST00000268912	T	0.00029	8.91	5.63	5.63	0.86233	GPCR, rhodopsin-like superfamily (1);	0.000000	0.32314	U	0.006262	T	0.00012	0.0000	N	0.04335	-0.225	0.34968	P	0.24717500000000003	B	0.31581	0.329	P	0.47075	0.536	T	0.04178	-1.0971	9	0.02654	T	1	-10.5232	12.168	0.54141	0.1708:0.8292:0.0:0.0	rs7218964;rs60643647;rs7218964	174	Q15615	OR4D1_HUMAN	I	174	ENSP00000365451:L174I	ENSP00000365451:L174I	L	+	1	2	OR4D1	53588033	0.000000	0.05858	0.984000	0.44739	0.100000	0.18952	-0.453000	0.06778	2.652000	0.90054	0.543000	0.68304	CTA	C|0.768;A|0.232	0.232	strong		0.542	OR4D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443364.1		
MFN2	9927	hgsc.bcm.edu	37	1	12065841	12065841	+	Silent	SNP	C	C	T	rs1042837	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr1:12065841C>T	ENST00000235329.5	+	15	1891	c.1569C>T	c.(1567-1569)tcC>tcT	p.S523S	MFN2_ENST00000444836.1_Silent_p.S523S	NM_014874.3	NP_055689.1	O95140	MFN2_HUMAN	mitofusin 2	523					apoptotic process (GO:0006915)|autophagy (GO:0006914)|blastocyst formation (GO:0001825)|blood coagulation (GO:0007596)|camera-type eye morphogenesis (GO:0048593)|mitochondrial fusion (GO:0008053)|mitochondrial membrane organization (GO:0007006)|mitochondrion localization (GO:0051646)|negative regulation of Ras protein signal transduction (GO:0046580)|negative regulation of smooth muscle cell proliferation (GO:0048662)|protein localization to pre-autophagosomal structure (GO:0034497)|protein targeting to mitochondrion (GO:0006626)|response to unfolded protein (GO:0006986)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|intrinsic component of mitochondrial outer membrane (GO:0031306)|microtubule cytoskeleton (GO:0015630)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|ubiquitin protein ligase binding (GO:0031625)			endometrium(4)|kidney(1)|large_intestine(4)|liver(2)|lung(3)|ovary(1)|pancreas(1)|prostate(2)|skin(2)	20	Ovarian(185;0.249)	Lung NSC(185;8.69e-05)|all_lung(284;9.87e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;7.25e-06)|COAD - Colon adenocarcinoma(227;0.000302)|BRCA - Breast invasive adenocarcinoma(304;0.000329)|Kidney(185;0.000896)|KIRC - Kidney renal clear cell carcinoma(229;0.00274)|STAD - Stomach adenocarcinoma(313;0.00773)|READ - Rectum adenocarcinoma(331;0.0656)		AGTGCTTCTCCCTCAACTATG	0.502													C|||	346	0.0690895	0.0159	0.0432	5008	,	,		24965	0.1389		0.0586	False		,,,				2504	0.0982				p.S523S		Atlas-SNP	.											MFN2,scalp,carcinoma,+1,1	MFN2	83	1	0			c.C1569T						scavenged	.	C	,	91,4315	74.1+/-112.3	3,85,2115	255.0	239.0	244.0		1569,1569	3.0	1.0	1	dbSNP_86	244	525,8075	147.4+/-202.8	15,495,3790	no	coding-synonymous,coding-synonymous	MFN2	NM_001127660.1,NM_014874.3	,	18,580,5905	TT,TC,CC		6.1047,2.0654,4.7363	,	523/758,523/758	12065841	616,12390	2203	4300	6503	SO:0001819	synonymous_variant	9927	exon15			CTTCTCCCTCAAC	AF036536	CCDS30587.1	1p36.22	2014-09-17			ENSG00000116688	ENSG00000116688			16877	protein-coding gene	gene with protein product		608507				12499352, 11181170	Standard	NM_014874		Approved	CPRP1, KIAA0214, MARF, CMT2A2	uc009vni.3	O95140	OTTHUMG00000002392	ENST00000235329.5:c.1569C>T	1.37:g.12065841C>T		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	108	4	0.037037	NM_014874	A8K1B3|O95572|Q5JXC3|Q5JXC4|Q9H131|Q9NSX8	Silent	SNP	ENST00000235329.5	37	CCDS30587.1																																																																																			C|0.946;T|0.054	0.054	strong		0.502	MFN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006859.2	NM_014874	
FAM120B	84498	hgsc.bcm.edu	37	6	170627883	170627883	+	Missense_Mutation	SNP	T	T	G	rs143059540	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr6:170627883T>G	ENST00000476287.1	+	2	1513	c.1405T>G	c.(1405-1407)Tcc>Gcc	p.S469A	FAM120B_ENST00000537664.1_Missense_Mutation_p.S492A|FAM120B_ENST00000540480.1_Missense_Mutation_p.S481A|FAM120B_ENST00000252510.9_Intron	NM_032448.1	NP_115824.1	Q96EK7	F120B_HUMAN	family with sequence similarity 120B	469					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)		AGGCCCTGAATCCAGGCAAGA	0.468																																					p.S469A		Atlas-SNP	.											FAM120B,NS,carcinoma,0,2	FAM120B	108	2	0			c.T1405G						scavenged	.						150.0	161.0	157.0					6																	170627883		2203	4300	6503	SO:0001583	missense	84498	exon2			CCTGAATCCAGGC	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.1405T>G	6.37:g.170627883T>G	ENSP00000417970:p.Ser469Ala	Somatic	179	4	0.0223464		WXS	Illumina HiSeq	Phase_I	157	11	0.0700637	NM_032448	B4DL34|Q86V68|Q96JI9	Missense_Mutation	SNP	ENST00000476287.1	37	CCDS5314.1	.	.	.	.	.	.	.	.	.	.	T	0.006	-2.023375	0.00414	.	.	ENSG00000112584	ENST00000540480;ENST00000537664;ENST00000476287	T;T;T	0.08370	3.13;3.1;3.13	1.31	-2.63	0.06133	.	1.867690	0.03051	N	0.154568	T	0.01287	0.0042	L	0.58101	1.795	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.53599	-0.8416	10	0.07644	T	0.81	.	2.1106	0.03702	0.1737:0.1223:0.1139:0.5901	.	469;469	Q96EK7;F2Z2E1	F120B_HUMAN;.	A	481;492;469	ENSP00000444125:S481A;ENSP00000440125:S492A;ENSP00000417970:S469A	ENSP00000436640:S469A	S	+	1	0	FAM120B	170469808	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-4.559000	0.00216	-6.111000	0.00006	-3.860000	0.00018	TCC	T|1.000;C|0.000	.	alt		0.468	FAM120B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000043259.2	NM_032448	
EXOC7	23265	hgsc.bcm.edu	37	17	74080183	74080183	+	Missense_Mutation	SNP	T	T	C			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr17:74080183T>C	ENST00000335146.7	-	19	2062	c.2009A>G	c.(2008-2010)cAg>cGg	p.Q670R	EXOC7_ENST00000411744.2_Missense_Mutation_p.Q611R|EXOC7_ENST00000607838.1_Missense_Mutation_p.Q642R|EXOC7_ENST00000589210.1_Missense_Mutation_p.Q619R|EXOC7_ENST00000332065.5_Missense_Mutation_p.Q588R|EXOC7_ENST00000467929.2_Missense_Mutation_p.Q591R|EXOC7_ENST00000405575.4_Missense_Mutation_p.Q628R|EXOC7_ENST00000591724.1_5'Flank			Q9UPT5	EXOC7_HUMAN	exocyst complex component 7	670					cellular protein metabolic process (GO:0044267)|exocytosis (GO:0006887)|membrane organization (GO:0061024)|protein transport (GO:0015031)	centriolar satellite (GO:0034451)|exocyst (GO:0000145)|growth cone membrane (GO:0032584)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|plasma membrane (GO:0005886)				NS(1)|breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|skin(1)	14			LUSC - Lung squamous cell carcinoma(166;0.187)			CCAGGCCTTCTGGATTTTGCA	0.522																																					p.Q670R		Atlas-SNP	.											.	EXOC7	47	.	0			c.A2009G						PASS	.						54.0	50.0	51.0					17																	74080183		2203	4300	6503	SO:0001583	missense	23265	exon19			GCCTTCTGGATTT	BC029432	CCDS11741.1, CCDS32738.1, CCDS45781.1, CCDS45782.1, CCDS45784.1, CCDS74164.1	17q25.3	2013-01-22			ENSG00000182473	ENSG00000182473			23214	protein-coding gene	gene with protein product		608163				12477932	Standard	NM_001013839		Approved	EXO70, KIAA1067, YJL085W, Exo70p	uc010wsw.2	Q9UPT5	OTTHUMG00000150720	ENST00000335146.7:c.2009A>G	17.37:g.74080183T>C	ENSP00000334100:p.Gln670Arg	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	73	25	0.342466	NM_001145297	B5MC69|B8XXP2|Q8ND93|Q8WV91|Q96FF0|Q9H8C3|Q9H9X3|Q9HA32	Missense_Mutation	SNP	ENST00000335146.7	37	CCDS45782.1	.	.	.	.	.	.	.	.	.	.	t	25.0	4.593561	0.86953	.	.	ENSG00000182473	ENST00000332065;ENST00000351709;ENST00000405575;ENST00000335146;ENST00000357231;ENST00000425372;ENST00000411744	.	.	.	5.28	5.28	0.74379	Cullin repeat-like-containing domain (1);	0.136469	0.51477	D	0.000088	T	0.80019	0.4547	M	0.80422	2.495	0.80722	D	1	D;D;D;D;D;D;D	0.89917	1.0;0.999;0.987;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D	0.97110	1.0;0.999;0.932;1.0;1.0;0.983;1.0	T	0.83105	-0.0126	9	0.72032	D	0.01	-24.4938	15.2203	0.73306	0.0:0.0:0.0:1.0	.	611;642;591;556;670;588;619	Q9UPT5-5;Q9UPT5-6;B4DJ07;F5H1P1;Q9UPT5;Q9UPT5-2;Q9UPT5-1	.;.;.;.;EXOC7_HUMAN;.;.	R	588;508;642;670;619;556;611	.	ENSP00000333806:Q588R	Q	-	2	0	EXOC7	71591778	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	7.843000	0.86859	2.000000	0.58554	0.449000	0.29647	CAG	.	.	none		0.522	EXOC7-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000319768.2	NM_015219	
PRDM1	639	hgsc.bcm.edu	37	6	106555025	106555025	+	Silent	SNP	G	G	A	rs1010273	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr6:106555025G>A	ENST00000369096.4	+	7	2376	c.2142G>A	c.(2140-2142)ccG>ccA	p.P714P	PRDM1_ENST00000369089.3_Silent_p.P580P|PRDM1_ENST00000369091.2_Silent_p.P678P	NM_001198.3	NP_001189.2	O75626	PRDM1_HUMAN	PR domain containing 1, with ZNF domain	714					cell fate commitment (GO:0045165)|eye photoreceptor cell development (GO:0042462)|germ cell development (GO:0007281)|intestinal epithelial cell development (GO:0060576)|maternal placenta development (GO:0001893)|negative regulation of B cell proliferation (GO:0030889)|negative regulation of lipopolysaccharide-mediated signaling pathway (GO:0031665)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of B cell differentiation (GO:0045579)|positive regulation of gene expression (GO:0010628)|post-embryonic development (GO:0009791)|transcription, DNA-templated (GO:0006351)|trophoblast giant cell differentiation (GO:0060707)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(59)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|skin(5)|urinary_tract(2)	94	Breast(9;0.022)	all_cancers(87;2.2e-31)|all_epithelial(87;2.03e-21)|Acute lymphoblastic leukemia(125;4.99e-11)|all_lung(197;7.55e-09)|all_hematologic(75;5.82e-08)|Lung NSC(302;1.28e-06)|Colorectal(196;0.0112)|Ovarian(999;0.0365)		all cancers(137;1.83e-46)|Epithelial(106;5.59e-35)|OV - Ovarian serous cystadenocarcinoma(136;1.99e-20)|GBM - Glioblastoma multiforme(226;3.72e-11)|BRCA - Breast invasive adenocarcinoma(108;1.38e-05)		CTGCGGCCCCGGCGCCTGGGC	0.577			"""D, N, Mis, F, S"""		DLBCL								G|||	457	0.091254	0.0197	0.0951	5008	,	,		19218	0.1865		0.1153	False		,,,				2504	0.0624				p.P714P		Atlas-SNP	.		Rec	yes		6	6q21	639	"""PR domain containing 1, with ZNF domain"""		L	.	PRDM1	195	.	0			c.G2142A						PASS	.	G	,	126,4280	91.1+/-129.8	3,120,2080	156.0	176.0	169.0		2142,1740	-11.9	0.0	6	dbSNP_86	169	857,7743	196.3+/-241.3	45,767,3488	no	coding-synonymous,coding-synonymous	PRDM1	NM_001198.3,NM_182907.1	,	48,887,5568	AA,AG,GG		9.9651,2.8597,7.5581	,	714/826,580/692	106555025	983,12023	2203	4300	6503	SO:0001819	synonymous_variant	639	exon7			GGCCCCGGCGCCT		CCDS5054.2, CCDS34505.1	6q21	2013-01-08			ENSG00000057657	ENSG00000057657		"""Zinc fingers, C2H2-type"""	9346	protein-coding gene	gene with protein product		603423		BLIMP1		1851123	Standard	NM_001198		Approved	PRDI-BF1	uc003prd.2	O75626	OTTHUMG00000015299	ENST00000369096.4:c.2142G>A	6.37:g.106555025G>A		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	62	4	0.0645161	NM_001198	B2REA6|E1P5E0|Q86WM7	Silent	SNP	ENST00000369096.4	37	CCDS5054.2																																																																																			G|0.910;A|0.090	0.090	strong		0.577	PRDM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041661.3		
LRIG1	26018	hgsc.bcm.edu	37	3	66430870	66430870	+	Silent	SNP	G	G	A	rs61754218	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr3:66430870G>A	ENST00000273261.3	-	19	3623	c.3099C>T	c.(3097-3099)tcC>tcT	p.S1033S	LRIG1_ENST00000496559.2_5'UTR|LRIG1_ENST00000383703.3_Silent_p.S1010S|SLC25A26_ENST00000536651.1_3'UTR	NM_015541.2	NP_056356.2	Q96JA1	LRIG1_HUMAN	leucine-rich repeats and immunoglobulin-like domains 1	1033					innervation (GO:0060384)|otolith morphogenesis (GO:0032474)|sensory perception of sound (GO:0007605)	integral component of membrane (GO:0016021)				NS(2)|breast(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(12)|ovary(3)|prostate(1)|skin(4)|stomach(4)|urinary_tract(1)	42		Lung NSC(201;0.0101)		BRCA - Breast invasive adenocarcinoma(55;0.00047)		GTAGCTCTGTGGAGTCCGGGT	0.527													G|||	223	0.0445288	0.003	0.0533	5008	,	,		19006	0.0179		0.0885	False		,,,				2504	0.0767				p.S1033S		Atlas-SNP	.											.	LRIG1	138	.	0			c.C3099T						PASS	.	G		72,4334	65.8+/-103.3	1,70,2132	109.0	113.0	112.0		3099	-0.2	0.0	3	dbSNP_129	112	611,7989	160.4+/-213.5	20,571,3709	no	coding-synonymous	LRIG1	NM_015541.2		21,641,5841	AA,AG,GG		7.1047,1.6341,5.2514		1033/1094	66430870	683,12323	2203	4300	6503	SO:0001819	synonymous_variant	26018	exon19			CTCTGTGGAGTCC	AB050468	CCDS33783.1	3p14	2013-01-14			ENSG00000144749	ENSG00000144749		"""Immunoglobulin superfamily / I-set domain containing"""	17360	protein-coding gene	gene with protein product	"""ortholog of mouse integral membrane glycoprotein LIG-1"", ""leucine-rich repeat protein LRIG1"""	608868				11414704, 12234026	Standard	NM_015541		Approved	LIG-1, DKFZP586O1624, LIG1	uc003dmx.3	Q96JA1	OTTHUMG00000158727	ENST00000273261.3:c.3099C>T	3.37:g.66430870G>A		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	84	4	0.047619	NM_015541	Q6IQ51|Q96CF9|Q9BYB8|Q9UFI4	Silent	SNP	ENST00000273261.3	37	CCDS33783.1																																																																																			A|0.049;C|0.000;G|0.950	0.049	strong		0.527	LRIG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351930.1	NM_015541	
SLCO2A1	6578	hgsc.bcm.edu	37	3	133698349	133698349	+	Silent	SNP	C	C	T	rs10935090	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr3:133698349C>T	ENST00000310926.4	-	2	483	c.210G>A	c.(208-210)tcG>tcA	p.S70S	SLCO2A1_ENST00000478651.1_5'UTR|SLCO2A1_ENST00000493729.1_Silent_p.S70S	NM_005630.2	NP_005621.2	Q92959	SO2A1_HUMAN	solute carrier organic anion transporter family, member 2A1	70					lipid transport (GO:0006869)|sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	lipid transporter activity (GO:0005319)|prostaglandin transmembrane transporter activity (GO:0015132)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(5)|lung(10)|ovary(1)|prostate(2)|skin(2)|stomach(2)	30					Alprostadil(DB00770)|Dinoprost Tromethamine(DB01160)|Dinoprostone(DB00917)|Furosemide(DB00695)|Iloprost(DB01088)|Phenobarbital(DB01174)|Pyruvic acid(DB00119)	AAATGAGACCCGATGAAGAAC	0.552													C|||	1278	0.255192	0.1241	0.1859	5008	,	,		21070	0.5357		0.1302	False		,,,				2504	0.3211				p.S70S		Atlas-SNP	.											.	SLCO2A1	72	.	0			c.G210A						PASS	.	C		536,3870	242.5+/-252.5	23,490,1690	147.0	143.0	144.0		210	-10.1	0.0	3	dbSNP_120	144	1142,7458	236.1+/-268.4	64,1014,3222	no	coding-synonymous	SLCO2A1	NM_005630.2		87,1504,4912	TT,TC,CC		13.2791,12.1652,12.9017		70/644	133698349	1678,11328	2203	4300	6503	SO:0001819	synonymous_variant	6578	exon2			GAGACCCGATGAA		CCDS3084.1	3q21	2013-05-22	2003-11-25	2003-11-26	ENSG00000174640	ENSG00000174640		"""Solute carriers"""	10955	protein-coding gene	gene with protein product		601460	"""solute carrier family 21 (prostaglandin transporter), member 2"", ""matrin F/G 1"""	SLC21A2, MATR1		8787677, 9618293	Standard	NM_005630		Approved	PGT, OATP2A1	uc003eqa.4	Q92959	OTTHUMG00000159745	ENST00000310926.4:c.210G>A	3.37:g.133698349C>T		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	91	4	0.043956	NM_005630	Q86V98|Q8IUN2	Silent	SNP	ENST00000310926.4	37	CCDS3084.1																																																																																			C|0.815;T|0.185	0.185	strong		0.552	SLCO2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357131.1	NM_005630	
C6orf47	57827	hgsc.bcm.edu	37	6	31627449	31627449	+	Missense_Mutation	SNP	C	C	G	rs2242655	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr6:31627449C>G	ENST00000375911.1	-	1	1100	c.276G>C	c.(274-276)aaG>aaC	p.K92N	C6orf47-AS1_ENST00000422049.1_RNA	NM_021184.3	NP_067007.3	O95873	CF047_HUMAN	chromosome 6 open reading frame 47	92			K -> N (in dbSNP:rs2242655).			cytoplasm (GO:0005737)				NS(1)|endometrium(1)|kidney(3)|large_intestine(1)|lung(1)|ovary(1)|skin(1)	9						GCTGGTCCCACTTGAGGGAAT	0.567													C|||	636	0.126997	0.0756	0.1873	5008	,	,		17694	0.131		0.163	False		,,,				2504	0.1125				p.K92N		Atlas-SNP	.											.	C6orf47	15	.	0			c.G276C						PASS	.	C	ASN/LYS	257,2763		12,233,1265	63.0	67.0	65.0		276	3.5	0.9	6	dbSNP_98	65	724,4694		52,620,2037	yes	missense	C6orf47	NM_021184.3	94	64,853,3302	GG,GC,CC		13.3629,8.5099,11.626	possibly-damaging	92/295	31627449	981,7457	1510	2709	4219	SO:0001583	missense	57827	exon1			GTCCCACTTGAGG	AF129756	CCDS34399.1	6p21.3	2011-12-13			ENSG00000204439	ENSG00000204439			19076	protein-coding gene	gene with protein product						2477242	Standard	NM_021184		Approved	D6S53E, G4	uc003nvm.1	O95873	OTTHUMG00000031172	ENST00000375911.1:c.276G>C	6.37:g.31627449C>G	ENSP00000365076:p.Lys92Asn	Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	89	5	0.0561798	NM_021184	B0UXA1|B0UZ50|Q5SSS6|Q95IG0	Missense_Mutation	SNP	ENST00000375911.1	37	CCDS34399.1	339	0.15521978021978022	33	0.06707317073170732	66	0.18232044198895028	103	0.18006993006993008	137	0.18073878627968337	C	13.06	2.125104	0.37533	0.085099	0.133629	ENSG00000204439	ENST00000375911;ENST00000538106	T	0.35236	1.32	5.44	3.53	0.40419	.	0.283163	0.25151	N	0.032743	T	0.29190	0.0726	L	0.54323	1.7	0.38932	P	0.04203599999999996	D	0.57257	0.979	P	0.54270	0.747	T	0.23332	-1.0191	9	0.72032	D	0.01	-7.2804	6.587	0.22626	0.0:0.7876:0.0:0.2124	rs2242655;rs17558921;rs58544317;rs2242655	92	O95873	CF047_HUMAN	N	92	ENSP00000365076:K92N	ENSP00000365076:K92N	K	-	3	2	C6orf47	31735428	0.307000	0.24500	0.857000	0.33713	0.849000	0.48306	0.439000	0.21575	1.541000	0.49316	0.655000	0.94253	AAG	C|0.866;G|0.134	0.134	strong		0.567	C6orf47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076324.1	NM_021184	
ZNF286B	729288	hgsc.bcm.edu	37	17	18565423	18565423	+	Missense_Mutation	SNP	G	G	A	rs9912852	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr17:18565423G>A	ENST00000545289.1	-	5	1646	c.1396C>T	c.(1396-1398)Ccg>Tcg	p.P466S	ZNF286B_ENST00000285274.5_3'UTR	NM_001145045.1	NP_001138517.1	P0CG31	Z286B_HUMAN	zinc finger protein 286B	466					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(1)|lung(1)	2						CATTTGTACGGTTTCTTTCCA	0.393													.|||	1375	0.274561	0.2027	0.4496	5008	,	,		22033	0.1935		0.4066	False		,,,				2504	0.1953				p.P466S		Atlas-SNP	.											ZNF286B_ENST00000545289,colon,carcinoma,+2,2	ZNF286B	75	2	0			c.C1396T						scavenged	.	G	SER/PRO	333,1051		41,251,400	137.0	131.0	133.0		1396	2.6	1.0	17	dbSNP_119	133	1243,1939		237,769,585	no	missense	ZNF286B	NM_001145045.1	74	278,1020,985	AA,AG,GG		39.0635,24.0607,34.516	probably-damaging	466/523	18565423	1576,2990	692	1591	2283	SO:0001583	missense	729288	exon5			TGTACGGTTTCTT		CCDS58523.1	17p11.2	2013-01-08			ENSG00000249459	ENSG00000249459		"""Zinc fingers, C2H2-type"""	33241	protein-coding gene	gene with protein product	"""zinc finger protein 590"""		"""zinc finger protein 286-like"", ""zinc finger 286C pseudogene"""	ZNF286L, ZNF286C			Standard	NM_001145045		Approved	ZNF590	uc010vyd.1	P0CG31	OTTHUMG00000178136	ENST00000545289.1:c.1396C>T	17.37:g.18565423G>A	ENSP00000461413:p.Pro466Ser	Somatic	261	1	0.00383142		WXS	Illumina HiSeq	Phase_I	254	6	0.023622	NM_001145045		Missense_Mutation	SNP	ENST00000545289.1	37	CCDS58523.1																																																																																			G|0.698;A|0.302	0.302	strong		0.393	ZNF286B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		XM_001723047	
ANKS1A	23294	hgsc.bcm.edu	37	6	34857324	34857324	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr6:34857324G>A	ENST00000360359.3	+	1	283	c.145G>A	c.(145-147)Ggc>Agc	p.G49S	TAF11_ENST00000361288.4_5'Flank|TAF11_ENST00000420584.2_5'Flank|ANKS1A_ENST00000535627.1_Missense_Mutation_p.G49S	NM_015245.2	NP_056060.2	Q92625	ANS1A_HUMAN	ankyrin repeat and sterile alpha motif domain containing 1A	49	Gly-rich.				ephrin receptor signaling pathway (GO:0048013)|neuron remodeling (GO:0016322)|substrate-dependent cell migration (GO:0006929)	cytoplasm (GO:0005737)|neuron projection (GO:0043005)|nucleus (GO:0005634)				cervix(2)|endometrium(3)|large_intestine(4)|lung(16)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	31						cggcagcggcggcggcggcgg	0.771																																					p.G49S		Atlas-SNP	.											ANKS1A,NS,carcinoma,0,1	ANKS1A	123	1	0			c.G145A						PASS	.						2.0	2.0	2.0					6																	34857324		382	1194	1576	SO:0001583	missense	23294	exon1			AGCGGCGGCGGCG	D86982	CCDS4798.1	6p21.31	2013-01-10	2006-02-17	2006-02-17	ENSG00000064999	ENSG00000064999		"""Sterile alpha motif (SAM) domain containing"", ""Ankyrin repeat domain containing"""	20961	protein-coding gene	gene with protein product		608994	"""ankyrin repeat and SAM domain containing 1"", ""ankyrin repeat and sterile alpha motif domain containing 1"""	ANKS1		9039502	Standard	NM_015245		Approved	KIAA0229	uc003ojx.4	Q92625	OTTHUMG00000014559	ENST00000360359.3:c.145G>A	6.37:g.34857324G>A	ENSP00000353518:p.Gly49Ser	Somatic	4	0	0		WXS	Illumina HiSeq	Phase_I	8	4	0.5	NM_015245	A2RUC1|B4DQW8|Q5JYI9|Q5SYR2|Q86WQ7	Missense_Mutation	SNP	ENST00000360359.3	37	CCDS4798.1	.	.	.	.	.	.	.	.	.	.	G	16.03	3.008376	0.54361	.	.	ENSG00000064999	ENST00000544150;ENST00000360359;ENST00000535627	T;D	0.98649	1.19;-5.05	4.58	1.53	0.23141	Ankyrin repeat-containing domain (1);	1.264600	0.06451	N	0.727796	D	0.90783	0.7106	N	0.19112	0.55	0.25322	N	0.989108	P;B	0.49090	0.919;0.003	B;B	0.38655	0.278;0.002	D	0.88474	0.3064	10	0.17832	T	0.49	-4.009	8.7007	0.34323	0.0795:0.0:0.6816:0.2389	.	49;49	B4DQW8;Q92625	.;ANS1A_HUMAN	S	49	ENSP00000353518:G49S;ENSP00000438752:G49S	ENSP00000353518:G49S	G	+	1	0	ANKS1A	34965302	1.000000	0.71417	0.794000	0.32065	0.327000	0.28475	2.586000	0.46119	0.389000	0.25086	0.471000	0.43371	GGC	.	.	none		0.771	ANKS1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040262.1	XM_166478	
KRT6C	286887	hgsc.bcm.edu	37	12	52863038	52863038	+	Silent	SNP	G	G	A	rs410562	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr12:52863038G>A	ENST00000252250.6	-	9	1550	c.1503C>T	c.(1501-1503)agC>agT	p.S501S		NM_173086.4	NP_775109.2	P48668	K2C6C_HUMAN	keratin 6C	501	Tail.				intermediate filament cytoskeleton organization (GO:0045104)	extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(6)|ovary(3)|prostate(2)|skin(2)	23				BRCA - Breast invasive adenocarcinoma(357;0.0828)		TGCCGACACCGCTGGCACCGC	0.612													G|||	1253	0.2502	0.0242	0.2651	5008	,	,		19993	0.4812		0.3628	False		,,,				2504	0.1912				p.S501S		Atlas-SNP	.											.	KRT6C	55	.	0			c.C1503T						PASS	.	G		314,4092	166.2+/-197.5	15,284,1904	42.0	40.0	41.0		1503	-6.3	0.0	12	dbSNP_80	41	3150,5450	457.5+/-364.3	579,1992,1729	no	coding-synonymous	KRT6C	NM_173086.4		594,2276,3633	AA,AG,GG		36.6279,7.1266,26.6339		501/565	52863038	3464,9542	2203	4300	6503	SO:0001819	synonymous_variant	286887	exon9			GACACCGCTGGCA	L42611	CCDS8829.1	12q13.13	2013-01-16	2006-07-17	2006-07-17	ENSG00000170465	ENSG00000170465		"""-"", ""Intermediate filaments type II, keratins (basic)"""	20406	protein-coding gene	gene with protein product		612315	"""keratin 6E"""	KRT6E		7543104, 16831889	Standard	NM_173086		Approved		uc001sal.4	P48668	OTTHUMG00000169596	ENST00000252250.6:c.1503C>T	12.37:g.52863038G>A		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	136	8	0.0588235	NM_173086	A1L4L5|P48666|Q2TAZ9|Q7RTN9	Silent	SNP	ENST00000252250.6	37	CCDS8829.1																																																																																			G|0.731;A|0.269	0.269	strong		0.612	KRT6C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404976.1	NM_173086	
ALK	238	hgsc.bcm.edu	37	2	29416481	29416481	+	Missense_Mutation	SNP	T	T	C	rs1881420	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr2:29416481T>C	ENST00000389048.3	-	29	5378	c.4472A>G	c.(4471-4473)aAg>aGg	p.K1491R	ALK_ENST00000431873.1_Missense_Mutation_p.K321R	NM_004304.4	NP_004295.2	Q9UM73	ALK_HUMAN	anaplastic lymphoma receptor tyrosine kinase	1491			K -> R (in dbSNP:rs1881420). {ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:9053841, ECO:0000269|Ref.4}.		activation of MAPK activity (GO:0000187)|cell proliferation (GO:0008283)|neuron development (GO:0048666)|NIK/NF-kappaB signaling (GO:0038061)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphorylation (GO:0016310)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein autophosphorylation (GO:0046777)|regulation of apoptotic process (GO:0042981)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|protein complex (GO:0043234)	ATP binding (GO:0005524)|NF-kappaB-inducing kinase activity (GO:0004704)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.K1491R(1)	ATIC/ALK(24)|FN1/ALK(2)|C2orf44/ALK(2)|TPM3/ALK(33)|KLC1/ALK(2)|VCL/ALK(4)|TPM4/ALK(12)|KIF5B/ALK(8)|RANBP2/ALK(34)|SQSTM1/ALK(2)|EML4/ALK(543)|PPFIBP1/ALK(3)|SEC31A/ALK(3)|NPM1/ALK(632)|CLTC/ALK(44)|CARS/ALK(5)|MSN/ALK(6)|TFG/ALK(9)	NS(2)|autonomic_ganglia(198)|breast(8)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(7)|kidney(4)|large_intestine(25)|lung(61)|ovary(6)|pancreas(1)|prostate(2)|skin(5)|soft_tissue(3)|stomach(2)|thyroid(2)	340	Acute lymphoblastic leukemia(172;0.155)				Adenosine triphosphate(DB00171)|Crizotinib(DB08865)	TCCGTGGACCTTGTGCAACTC	0.532			"""T, Mis, A"""	"""NPM1, TPM3, TFG, TPM4, ATIC, CLTC, MSN, ALO17, CARS, EML4, KIF5B, C2orf22"""	"""ALCL, NSCLC, Neuroblastoma"""	neuroblastoma			Neuroblastoma, Familial Clustering of;Congenital Central Hypoventilation Syndrome				T|||	2079	0.415136	0.2405	0.4467	5008	,	,		18547	0.7312		0.2336	False		,,,				2504	0.4898				p.K1491R		Atlas-SNP	.	yes	Dom	yes	Familial neuroblastoma	2	2p23	238	anaplastic lymphoma kinase (Ki-1)		"""L, E, M"""	ALK,NS,carcinoma,0,1	ALK	533	1	1	Substitution - Missense(1)	prostate(1)	c.A4472G						scavenged	.		ARG/LYS	1068,3338	389.1+/-327.2	147,774,1282	113.0	118.0	116.0		4472	1.9	0.4	2	dbSNP_92	116	1837,6763	330.1+/-319.0	216,1405,2679	yes	missense	ALK	NM_004304.4	26	363,2179,3961	CC,CT,TT		21.3605,24.2397,22.3358	benign	1491/1621	29416481	2905,10101	2203	4300	6503	SO:0001583	missense	238	exon29	Familial Cancer Database	Familial Neuroblastoma;CCHS, Ondine Curse, incl. Ondine-Hirschsprung Disease	TGGACCTTGTGCA	D45915	CCDS33172.1	2p23	2014-09-17	2008-01-23		ENSG00000171094	ENSG00000171094		"""CD molecules"""	427	protein-coding gene	gene with protein product		105590	"""anaplastic lymphoma kinase (Ki-1)"""			8122112	Standard	NM_004304		Approved	CD246	uc002rmy.3	Q9UM73	OTTHUMG00000152034	ENST00000389048.3:c.4472A>G	2.37:g.29416481T>C	ENSP00000373700:p.Lys1491Arg	Somatic	207	1	0.00483092		WXS	Illumina HiSeq	Phase_I	180	3	0.0166667	NM_004304	Q4ZFX9|Q53QQ6|Q53RZ4|Q59FI3|Q9Y4K6	Missense_Mutation	SNP	ENST00000389048.3	37	CCDS33172.1	863	0.39514652014652013	114	0.23170731707317074	151	0.4171270718232044	415	0.7255244755244755	183	0.24142480211081793	t	13.96	2.391818	0.42410	0.242397	0.213605	ENSG00000171094	ENST00000389048;ENST00000431873	T;T	0.77489	-1.1;2.84	5.64	1.9	0.25705	.	0.124743	0.35349	U	0.003264	T	0.00012	0.0000	L	0.60455	1.87	0.51233	P	8.500000000000174E-5	B	0.02656	0.0	B	0.08055	0.003	T	0.44467	-0.9326	9	0.23302	T	0.38	.	6.8496	0.24008	0.0:0.1336:0.1271:0.7393	rs1881420;rs3738871;rs56441963;rs59805402;rs1881420	1491	Q9UM73	ALK_HUMAN	R	1491;321	ENSP00000373700:K1491R;ENSP00000414027:K321R	ENSP00000373700:K1491R	K	-	2	0	ALK	29269985	1.000000	0.71417	0.353000	0.25747	0.942000	0.58702	2.447000	0.44917	0.089000	0.17243	0.454000	0.30748	AAG	T|0.684;G|0.005	.	strong		0.532	ALK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324994.1	NM_004304	
DMXL2	23312	hgsc.bcm.edu	37	15	51772895	51772895	+	Silent	SNP	G	G	T	rs78376092	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr15:51772895G>T	ENST00000251076.5	-	24	6695	c.6408C>A	c.(6406-6408)gcC>gcA	p.A2136A	DMXL2_ENST00000543779.2_Silent_p.A2136A|RP11-707P17.1_ENST00000561007.1_RNA|DMXL2_ENST00000449909.3_Silent_p.A1500A	NM_001174116.1|NM_015263.3	NP_001167587.1|NP_056078.2	Q8TDJ6	DMXL2_HUMAN	Dmx-like 2	2136						cell junction (GO:0030054)|extracellular space (GO:0005615)|membrane (GO:0016020)|synaptic vesicle (GO:0008021)	Rab GTPase binding (GO:0017137)			breast(4)|central_nervous_system(1)|cervix(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(26)|liver(1)|lung(28)|ovary(7)|prostate(7)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	101				all cancers(107;0.00494)		GCTCTCGTTTGGCCTGCAATC	0.458													G|||	59	0.0117812	0.0015	0.0029	5008	,	,		19487	0.0288		0.0129	False		,,,				2504	0.0133				p.A2136A		Atlas-SNP	.											DMXL2,NS,carcinoma,-1,1	DMXL2	262	1	0			c.C6408A						scavenged	.	G	,,	12,4380	19.1+/-41.9	0,12,2184	139.0	131.0	133.0		6408,4500,6408	-6.2	0.8	15	dbSNP_131	133	151,8435	73.5+/-136.2	2,147,4144	no	coding-synonymous,coding-synonymous,coding-synonymous	DMXL2	NM_001174116.1,NM_001174117.1,NM_015263.3	,,	2,159,6328	TT,TG,GG		1.7587,0.2732,1.256	,,	2136/3038,1500/2401,2136/3037	51772895	163,12815	2196	4293	6489	SO:0001819	synonymous_variant	23312	exon24			TCGTTTGGCCTGC	AB020663	CCDS10141.1, CCDS53945.1, CCDS53946.1	15q21.2	2013-01-10			ENSG00000104093	ENSG00000104093		"""WD repeat domain containing"""	2938	protein-coding gene	gene with protein product	"""rabconnectin 3"""	612186					Standard	NM_001174116		Approved	RC3, KIAA0856	uc010ufy.2	Q8TDJ6	OTTHUMG00000131749	ENST00000251076.5:c.6408C>A	15.37:g.51772895G>T		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	137	3	0.0218978	NM_001174116	B2RTR3|B7ZMH3|F5GWF1|O94938	Silent	SNP	ENST00000251076.5	37	CCDS10141.1																																																																																			G|0.987;T|0.013	0.013	strong		0.458	DMXL2-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254671.2	NM_015263	
ZNF502	91392	hgsc.bcm.edu	37	3	44763037	44763037	+	Missense_Mutation	SNP	A	A	C	rs7640654	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr3:44763037A>C	ENST00000296091.4	+	4	984	c.728A>C	c.(727-729)gAa>gCa	p.E243A	ZNF502_ENST00000449836.1_Missense_Mutation_p.E243A|ZNF502_ENST00000436624.2_Missense_Mutation_p.E243A	NM_001134440.1|NM_001282880.1|NM_033210.4	NP_001127912.1|NP_001269809.1|NP_149987.2	Q8TBZ5	ZN502_HUMAN	zinc finger protein 502	243			E -> A (in dbSNP:rs7640654).		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(4)|large_intestine(8)|lung(4)|prostate(1)|urinary_tract(1)	19				BRCA - Breast invasive adenocarcinoma(193;0.00855)|KIRC - Kidney renal clear cell carcinoma(197;0.0471)|Kidney(197;0.0589)		AAATGCAATGAATGTGGGAAT	0.413													A|||	2697	0.538538	0.208	0.5288	5008	,	,		22772	0.8353		0.5219	False		,,,				2504	0.7035				p.E243A		Atlas-SNP	.											.	ZNF502	58	.	0			c.A728C						PASS	.	A	ALA/GLU,ALA/GLU,ALA/GLU,ALA/GLU	1140,3266	402.4+/-332.3	164,812,1227	102.0	108.0	106.0		728,728,728,728	3.6	0.5	3	dbSNP_116	106	4210,4390	567.0+/-388.8	1016,2178,1106	yes	missense,missense,missense,missense	ZNF502	NM_001134440.1,NM_001134441.1,NM_001134442.1,NM_033210.4	107,107,107,107	1180,2990,2333	CC,CA,AA		48.9535,25.8738,41.1349	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	243/545,243/545,243/545,243/545	44763037	5350,7656	2203	4300	6503	SO:0001583	missense	91392	exon4			GCAATGAATGTGG	AK022577	CCDS2719.1	3p21.32	2013-01-08			ENSG00000196653	ENSG00000196653		"""Zinc fingers, C2H2-type"""	23718	protein-coding gene	gene with protein product							Standard	NM_033210		Approved	FLJ14855, FLJ12515	uc003cnt.3	Q8TBZ5	OTTHUMG00000133086	ENST00000296091.4:c.728A>C	3.37:g.44763037A>C	ENSP00000296091:p.Glu243Ala	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	83	5	0.060241	NM_001134440		Missense_Mutation	SNP	ENST00000296091.4	37	CCDS2719.1	1200|1200	0.5494505494505495|0.5494505494505495	112|112	0.22764227642276422|0.22764227642276422	205|205	0.5662983425414365|0.5662983425414365	492|492	0.8601398601398601|0.8601398601398601	391|391	0.5158311345646438|0.5158311345646438	A|A	15.41|15.41	2.824378|2.824378	0.50739|0.50739	0.258738|0.258738	0.489535|0.489535	ENSG00000196653|ENSG00000196653	ENST00000449836;ENST00000296091;ENST00000436624|ENST00000427783	T;T;T|.	0.01165|.	5.24;5.24;5.24|.	3.63|3.63	3.63|3.63	0.41609|0.41609	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.49571|0.49571	1.57|1.57	0.58432|0.58432	P|P	5.000000000032756E-6|5.000000000032756E-6	B|.	0.19200|.	0.034|.	B|.	0.29176|.	0.099|.	T|T	0.09228|0.09228	-1.0684|-1.0684	8|5	0.72032|0.62326	D|D	0.01|0.03	-6.1294|-6.1294	12.1883|12.1883	0.54252|0.54252	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	rs7640654;rs52823982;rs59529674;rs7640654|rs7640654;rs52823982;rs59529674;rs7640654	243|.	Q8TBZ5|.	ZN502_HUMAN|.	A|H	243|243	ENSP00000397390:E243A;ENSP00000296091:E243A;ENSP00000406469:E243A|.	ENSP00000296091:E243A|ENSP00000397812:N243H	E|N	+|+	2|1	0|0	ZNF502|ZNF502	44738041|44738041	0.005000|0.005000	0.15991|0.15991	0.519000|0.519000	0.27824|0.27824	0.952000|0.952000	0.60782|0.60782	2.020000|2.020000	0.41010|0.41010	1.899000|1.899000	0.54978|0.54978	0.533000|0.533000	0.62120|0.62120	GAA|AAT	A|0.537;C|0.463	0.463	strong		0.413	ZNF502-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256744.4	NM_033210	
MUC5B	727897	hgsc.bcm.edu	37	11	1268064	1268064	+	Silent	SNP	C	C	T	rs200948102	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr11:1268064C>T	ENST00000529681.1	+	31	10012	c.9954C>T	c.(9952-9954)gcC>gcT	p.A3318A	MUC5B_ENST00000447027.1_Silent_p.A3321A|RP11-532E4.2_ENST00000532061.2_RNA	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	3318	17 X approximate tandem repeats, Ser/Thr- rich.|7 X Cys-rich subdomain repeats.|Thr-rich.			Missing (in Ref. 6; AAB61398). {ECO:0000305}.	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)		GCTTCACAGCCACCCCCTCCT	0.652													c|||	1636	0.326677	0.2156	0.3256	5008	,	,		19867	0.5387		0.2853	False		,,,				2504	0.3016				p.A3318A		Atlas-SNP	.											MUC5B,NS,carcinoma,0,2	MUC5B	473	2	0			c.C9954T						scavenged	.						15.0	28.0	24.0					11																	1268064		1776	4009	5785	SO:0001819	synonymous_variant	727897	exon31			CACAGCCACCCCC	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.9954C>T	11.37:g.1268064C>T		Somatic	214	0	0		WXS	Illumina HiSeq	Phase_I	275	5	0.0181818	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Silent	SNP	ENST00000529681.1	37	CCDS44515.2	.	.	.	.	.	.	.	.	.	.	C	3.753	-0.051234	0.07407	.	.	ENSG00000117983	ENST00000538459	.	.	.	3.18	0.963	0.19649	.	.	.	.	.	T	0.15392	0.0371	.	.	.	0.58432	P	1.0000000000287557E-6	.	.	.	.	.	.	T	0.38908	-0.9639	4	0.02654	T	1	.	6.2137	0.20644	0.3708:0.4477:0.1814:0.0	.	.	.	.	Y	201	.	ENSP00000442622:H201Y	H	+	1	0	MUC5B	1224640	0.000000	0.05858	0.001000	0.08648	0.030000	0.12068	-0.998000	0.03701	-0.041000	0.13558	0.305000	0.20034	CAC	C|0.846;T|0.154	0.154	strong		0.652	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
OR52D1	390066	hgsc.bcm.edu	37	11	5510809	5510809	+	Silent	SNP	C	C	T			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr11:5510809C>T	ENST00000322641.5	+	1	895	c.873C>T	c.(871-873)ctC>ctT	p.L291L	HBG2_ENST00000380252.1_Intron|HBE1_ENST00000380237.1_Intron|HBG2_ENST00000380259.2_Intron|AC104389.28_ENST00000415970.1_RNA	NM_001005163.2	NP_001005163.1	Q9H346	O52D1_HUMAN	olfactory receptor, family 52, subfamily D, member 1	291					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)			central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(5)|lung(8)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	22		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;3.46e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		CTCCTGTACTCAATCCTATTC	0.483																																					p.L291L		Atlas-SNP	.											OR52D1,NS,carcinoma,0,1	OR52D1	66	1	0			c.C873T						scavenged	.						95.0	86.0	89.0					11																	5510809		2201	4297	6498	SO:0001819	synonymous_variant	390066	exon1			TGTACTCAATCCT	BK004276	CCDS31384.1	11p15.4	2012-08-09			ENSG00000181609	ENSG00000181609		"""GPCR / Class A : Olfactory receptors"""	15212	protein-coding gene	gene with protein product							Standard	NM_001005163		Approved		uc010qzg.2	Q9H346	OTTHUMG00000066895	ENST00000322641.5:c.873C>T	11.37:g.5510809C>T		Somatic	228	0	0		WXS	Illumina HiSeq	Phase_I	260	7	0.0269231	NM_001005163	B9EGY9|Q6IFI6	Silent	SNP	ENST00000322641.5	37	CCDS31384.1																																																																																			.	.	none		0.483	OR52D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143372.1	NM_001005163	
HIST1H2BK	85236	hgsc.bcm.edu	37	6	27114569	27114569	+	Silent	SNP	T	T	C			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr6:27114569T>C	ENST00000356950.1	-	1	8	c.9A>G	c.(7-9)gaA>gaG	p.E3E	HIST1H2AH_ENST00000377459.1_5'Flank|HIST1H2BK_ENST00000396891.4_Silent_p.E3E|MIR3143_ENST00000584253.1_RNA			O60814	H2B1K_HUMAN	histone cluster 1, H2bk	3					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						ACTTCGCTGGTTCCGGCATGT	0.562																																					p.E3E		Atlas-SNP	.											HIST1H2BK_ENST00000396891,NS,carcinoma,-2,2	HIST1H2BK	68	2	0			c.A9G						scavenged	.						51.0	51.0	51.0					6																	27114569		2203	4300	6503	SO:0001819	synonymous_variant	85236	exon1			CGCTGGTTCCGGC	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.9A>G	6.37:g.27114569T>C		Somatic	108	5	0.0462963		WXS	Illumina HiSeq	Phase_I	91	7	0.0769231	NM_080593	A8K7P7|Q2VPI7	Silent	SNP	ENST00000356950.1	37	CCDS4621.1																																																																																			.	.	none		0.562	HIST1H2BK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040141.1	NM_080593	
HTT	3064	hgsc.bcm.edu	37	4	3227419	3227419	+	Silent	SNP	A	A	G	rs362273	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr4:3227419A>G	ENST00000355072.5	+	57	7942	c.7797A>G	c.(7795-7797)ctA>ctG	p.L2599L		NM_002111.6	NP_002102	P42858	HD_HUMAN	huntingtin	2599					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)		AGCTGCTGCTACAGATCAACC	0.647													G|||	1234	0.246406	0.1218	0.304	5008	,	,		14498	0.3393		0.3191	False		,,,				2504	0.2035				p.L2599L		Atlas-SNP	.											HTT,caecum,carcinoma,0,1	HTT	221	1	0			c.A7797G						scavenged	.	G		636,3396		56,524,1436	28.0	32.0	31.0		7797	3.1	1.0	4	dbSNP_79	31	2492,5908		355,1782,2063	no	coding-synonymous	HTT	NM_002111.6		411,2306,3499	GG,GA,AA		29.6667,15.7738,25.1609		2599/3143	3227419	3128,9304	2016	4200	6216	SO:0001819	synonymous_variant	3064	exon57			GCTGCTACAGATC	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.7797A>G	4.37:g.3227419A>G		Somatic	173	1	0.00578035		WXS	Illumina HiSeq	Phase_I	170	5	0.0294118	NM_002111	Q9UQB7	Silent	SNP	ENST00000355072.5	37	CCDS43206.1																																																																																			A|0.737;G|0.263	0.263	strong		0.647	HTT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358234.2	NM_002111	
CFAP70	118491	hgsc.bcm.edu	37	10	75056863	75056863	+	Silent	SNP	A	A	C	rs6480692	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr10:75056863A>C	ENST00000310715.3	-	16	1911	c.1791T>G	c.(1789-1791)ctT>ctG	p.L597L	TTC18_ENST00000340329.3_Intron|TTC18_ENST00000493787.1_5'UTR|TTC18_ENST00000394865.1_Silent_p.L597L|TTC18_ENST00000355577.3_Silent_p.L66L|TTC18_ENST00000401621.2_Silent_p.L597L	NM_145170.3	NP_660153.3	Q5T0N1	TTC18_HUMAN		597						extracellular vesicular exosome (GO:0070062)		p.L597L(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(13)|ovary(2)|prostate(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	34	Prostate(51;0.0119)					TAAATGTCTGAAGTTCCTCCT	0.403													C|||	890	0.177716	0.177	0.0994	5008	,	,		19536	0.3105		0.0547	False		,,,				2504	0.2239				p.L597L		Atlas-SNP	.											TTC18,NS,carcinoma,-2,2	TTC18	106	2	1	Substitution - coding silent(1)	stomach(1)	c.T1791G						scavenged	.	C		659,3747	764.7+/-413.3	56,547,1600	222.0	199.0	207.0		1791	0.0	1.0	10	dbSNP_116	207	573,8027	793.6+/-407.5	27,519,3754	no	coding-synonymous	TTC18	NM_145170.3		83,1066,5354	CC,CA,AA		6.6628,14.9569,9.4726		597/1122	75056863	1232,11774	2203	4300	6503	SO:0001819	synonymous_variant	118491	exon16			TGTCTGAAGTTCC																												ENST00000310715.3:c.1791T>G	10.37:g.75056863A>C		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	110	3	0.0272727	NM_145170	C9JIZ9|Q5T0M4|Q5T0M9|Q5T0N0|Q69YH9|Q8IYZ8|Q8N7D5|Q8NI30|Q8NI31	Silent	SNP	ENST00000310715.3	37	CCDS7324.3																																																																																			A|0.870;C|0.130	0.130	strong		0.403	TTC18-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding			
TCN2	6948	hgsc.bcm.edu	37	22	31011610	31011610	+	Missense_Mutation	SNP	G	G	C	rs1801198	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr22:31011610G>C	ENST00000215838.3	+	6	1270	c.776G>C	c.(775-777)cGt>cCt	p.R259P	TCN2_ENST00000407817.3_Missense_Mutation_p.R232P|TCN2_ENST00000405742.3_Missense_Mutation_p.R255P			P20062	TCO2_HUMAN	transcobalamin II	259			R -> P (in dbSNP:rs1801198). {ECO:0000269|PubMed:11159542, ECO:0000269|PubMed:15461802, ECO:0000269|PubMed:1708393}.		cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|cobalt ion transport (GO:0006824)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	endosome (GO:0005768)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)	cobalamin binding (GO:0031419)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(6)|prostate(2)|urinary_tract(1)	22					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	TCCCCCATGCGTGGGGCAGAA	0.572													C|||	2903	0.579673	0.7814	0.6441	5008	,	,		20269	0.4444		0.5716	False		,,,				2504	0.409				p.R259P		Atlas-SNP	.											.	TCN2	44	.	0			c.G776C	GRCh37	CM022466	TCN2	M	rs1801198	PASS	.	C	PRO/ARG,PRO/ARG	3372,1034	384.7+/-325.4	1294,784,125	67.0	60.0	62.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	776,695	4.1	0.0	22	dbSNP_89	62	4865,3735	532.5+/-382.2	1398,2069,833	yes	missense,missense	TCN2	NM_000355.3,NM_001184726.1	103,103	2692,2853,958	CC,CG,GG		43.4302,23.468,36.6677	benign,benign	259/428,232/401	31011610	8237,4769	2203	4300	6503	SO:0001583	missense	6948	exon6			CCATGCGTGGGGC		CCDS13881.1, CCDS54519.1	22q12.2	2014-09-17	2010-05-11		ENSG00000185339	ENSG00000185339			11653	protein-coding gene	gene with protein product	"""macrocytic anemia"""	613441	"""transcobalamin II; macrocytic anemia"""			1708393, 7742531	Standard	NM_000355		Approved	D22S676, D22S750, TC2	uc003aip.2	P20062	OTTHUMG00000151095	ENST00000215838.3:c.776G>C	22.37:g.31011610G>C	ENSP00000215838:p.Arg259Pro	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	65	4	0.0615385	NM_000355	Q96FD4|Q9BVI8|Q9UCI5|Q9UCI6|Q9UDM0	Missense_Mutation	SNP	ENST00000215838.3	37	CCDS13881.1	1282	0.586996336996337	381	0.774390243902439	210	0.580110497237569	261	0.4562937062937063	430	0.5672823218997362	C	0.376	-0.931342	0.02359	0.76532	0.565698	ENSG00000185339	ENST00000215838;ENST00000405742;ENST00000407817	T;T;T	0.33438	1.41;1.41;1.41	5.15	4.13	0.48395	.	1.169260	0.05803	N	0.612573	T	0.00012	0.0000	N	0.00823	-1.155	0.54753	P	1.0999999999983245E-5	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.41052	-0.9530	9	0.11485	T	0.65	-2.4631	13.2458	0.60022	0.0:0.6946:0.3054:0.0	rs1801198;rs11557598;rs57035094;rs1801198	232;255;259	Q96FD4;B5MBX2;P20062	.;.;TCO2_HUMAN	P	259;255;232	ENSP00000215838:R259P;ENSP00000385914:R255P;ENSP00000384914:R232P	ENSP00000215838:R259P	R	+	2	0	TCN2	29341610	0.000000	0.05858	0.001000	0.08648	0.000000	0.00434	0.146000	0.16180	0.766000	0.33244	-0.216000	0.12614	CGT	G|0.390;C|0.610	0.610	strong		0.572	TCN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000321282.2	NM_000355	
CYP2A7	1549	hgsc.bcm.edu	37	19	41386136	41386136	+	Missense_Mutation	SNP	A	A	C	rs4142867	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr19:41386136A>C	ENST00000301146.4	-	4	1048	c.507T>G	c.(505-507)gaT>gaG	p.D169E	CYP2A7_ENST00000291764.3_Missense_Mutation_p.D118E|CTC-490E21.12_ENST00000601627.1_Intron	NM_000764.2	NP_000755.2	P20853	CP2A7_HUMAN	cytochrome P450, family 2, subfamily A, polypeptide 7	169			D -> E (in dbSNP:rs4142867).			endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxygen binding (GO:0019825)	p.D169E(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(6)|lung(7)|ovary(4)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)			AGAAGGTGGGATCGATATTGG	0.547													.|||	2600	0.519169	0.4251	0.6758	5008	,	,		15007	0.4395		0.5189	False		,,,				2504	0.6176				p.D169E		Atlas-SNP	.											CYP2A7,NS,carcinoma,0,1	CYP2A7	71	1	1	Substitution - Missense(1)	prostate(1)	c.T507G						scavenged	.	A	GLU/ASP,GLU/ASP	1977,2429	557.6+/-379.8	447,1083,673	112.0	100.0	104.0		507,354	-0.2	0.7	19	dbSNP_110	104	4355,4245	580.8+/-391.1	1124,2107,1069	no	missense,missense	CYP2A7	NM_000764.2,NM_030589.2	45,45	1571,3190,1742	CC,CA,AA		49.3605,44.8706,48.6852	benign,benign	169/495,118/444	41386136	6332,6674	2203	4300	6503	SO:0001583	missense	1549	exon4			GGTGGGATCGATA	NM_000764	CCDS12569.1, CCDS42570.1	19q13.2	2013-07-25	2003-01-14		ENSG00000198077	ENSG00000198077		"""Cytochrome P450s"""	2611	protein-coding gene	gene with protein product		608054	"""cytochrome P450, subfamily IIA (phenobarbital-inducible), polypeptide 7"""			7668294, 15128046	Standard	NM_030589		Approved	CYP2A	uc002opm.3	P20853	OTTHUMG00000182715	ENST00000301146.4:c.507T>G	19.37:g.41386136A>C	ENSP00000301146:p.Asp169Glu	Somatic	172	1	0.00581395		WXS	Illumina HiSeq	Phase_I	152	3	0.0197368	NM_000764	Q13121	Missense_Mutation	SNP	ENST00000301146.4	37	CCDS12569.1	1113	0.5096153846153846	206	0.4186991869918699	248	0.6850828729281768	268	0.46853146853146854	391	0.5158311345646438	a	11.54	1.669766	0.29693	0.448706	0.506395	ENSG00000198077	ENST00000301146;ENST00000291764	T;T	0.72505	-0.66;-0.66	2.2	-0.181	0.13291	.	0.176525	0.46758	U	0.000274	T	0.00012	0.0000	M	0.68593	2.085	0.49483	P	2.0699999999995722E-4	B;B;B	0.29862	0.017;0.128;0.259	B;B;B	0.36134	0.014;0.098;0.218	T	0.38520	-0.9657	9	0.59425	D	0.04	.	5.7105	0.17933	0.7168:0.0:0.2832:0.0	rs4142867	169;118;169	B7ZKR0;F8W816;P20853	.;.;CP2A7_HUMAN	E	169;118	ENSP00000301146:D169E;ENSP00000291764:D118E	ENSP00000291764:D118E	D	-	3	2	CYP2A7	46077976	0.310000	0.24527	0.715000	0.30552	0.201000	0.24016	-0.547000	0.06055	-0.239000	0.09710	0.157000	0.16456	GAT	A|0.502;C|0.498	0.498	strong		0.547	CYP2A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463269.2	NM_030589	
OSBPL7	114881	hgsc.bcm.edu	37	17	45885756	45885756	+	Silent	SNP	C	C	T	rs9911983	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr17:45885756C>T	ENST00000007414.3	-	23	2621	c.2430G>A	c.(2428-2430)acG>acA	p.T810T	OSBPL7_ENST00000392507.3_Silent_p.T810T	NM_145798.2	NP_665741.1	Q9BZF2	OSBL7_HUMAN	oxysterol binding protein-like 7	810					cellular response to cholesterol (GO:0071397)|lipid transport (GO:0006869)|positive regulation of proteasomal protein catabolic process (GO:1901800)	autophagic vacuole (GO:0005776)|cytosol (GO:0005829)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)	cholesterol binding (GO:0015485)			autonomic_ganglia(1)|endometrium(6)|kidney(2)|large_intestine(5)|liver(2)|lung(13)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	32						CGCTGCTATCCGTCTGCCGCC	0.627													T|||	2374	0.474042	0.7005	0.4352	5008	,	,		19535	0.1528		0.5298	False		,,,				2504	0.4693				p.T810T		Atlas-SNP	.											OSBPL7,colon,carcinoma,-1,1	OSBPL7	65	1	0			c.G2430A						PASS	.	T		3093,1313	444.5+/-347.4	1094,905,204	61.0	56.0	58.0		2430	-8.4	0.8	17	dbSNP_119	58	4785,3815	538.2+/-383.4	1362,2061,877	no	coding-synonymous	OSBPL7	NM_145798.2		2456,2966,1081	TT,TC,CC		44.3605,29.8003,39.428		810/843	45885756	7878,5128	2203	4300	6503	SO:0001819	synonymous_variant	114881	exon23			GCTATCCGTCTGC	AF392446	CCDS11515.1	17q21	2013-01-10				ENSG00000006025		"""Oxysterol binding proteins"", ""Pleckstrin homology (PH) domain containing"""	16387	protein-coding gene	gene with protein product		606735				14593528, 11735225	Standard	NM_145798		Approved	ORP7, MGC71150	uc002ilx.1	Q9BZF2		ENST00000007414.3:c.2430G>A	17.37:g.45885756C>T		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	88	5	0.0568182	NM_145798	D3DTT6|Q6PIV6	Silent	SNP	ENST00000007414.3	37	CCDS11515.1																																																																																			C|0.449;T|0.551	0.551	strong		0.627	OSBPL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441367.1	NM_017731	
DNAH14	127602	hgsc.bcm.edu	37	1	225534348	225534348	+	Missense_Mutation	SNP	G	G	A	rs7535953	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr1:225534348G>A	ENST00000445597.2	+	49	8600	c.8600G>A	c.(8599-8601)aGa>aAa	p.R2867K	DNAH14_ENST00000439375.2_Missense_Mutation_p.R3670K|DNAH14_ENST00000430092.1_Missense_Mutation_p.R3670K			Q0VDD8	DYH14_HUMAN	dynein, axonemal, heavy chain 14	2867					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						TCCCAGTCTAGACTTACTAGT	0.338													G|||	2650	0.529153	0.6407	0.4697	5008	,	,		17939	0.5089		0.4046	False		,,,				2504	0.5695				p.R3670K		Atlas-SNP	.											.	DNAH14	300	.	0			c.G11009A						PASS	.						48.0	44.0	45.0					1																	225534348		692	1585	2277	SO:0001583	missense	127602	exon69			AGTCTAGACTTAC	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.8600G>A	1.37:g.225534348G>A	ENSP00000409472:p.Arg2867Lys	Somatic	198	0	0		WXS	Illumina HiSeq	Phase_I	144	6	0.0416667	NM_001373	A6NG62|A6NNL2|Q0VDD9|Q4VXC7|Q4VXG4|Q4VXG5|Q5VU33|Q5VU34	Missense_Mutation	SNP	ENST00000445597.2	37		1054	0.4826007326007326	302	0.6138211382113821	165	0.4558011049723757	281	0.49125874125874125	306	0.40369393139841686	G	1.991	-0.431729	0.04669	.	.	ENSG00000185842	ENST00000445597;ENST00000430092;ENST00000439375	T;T;T	0.39997	1.05;1.05;1.05	4.94	-3.81	0.04294	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.06786	0.001	B	0.06405	0.002	T	0.40213	-0.9575	7	0.02654	T	1	.	6.7277	0.23365	0.6059:0.0:0.272:0.1221	rs7535953;rs17522510;rs52812222;rs58063527;rs7535953	3670	Q0VDD8-4	.	K	2867;3670;3670	ENSP00000409472:R2867K;ENSP00000414402:R3670K;ENSP00000392061:R3670K	ENSP00000414402:R3670K	R	+	2	0	DNAH14	223600971	0.000000	0.05858	0.000000	0.03702	0.463000	0.32649	-0.207000	0.09384	-0.823000	0.04301	-0.357000	0.07601	AGA	G|0.499;A|0.501	0.501	strong		0.338	DNAH14-007	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000331217.3	XM_059166	
ARHGAP42	143872	hgsc.bcm.edu	37	11	100846936	100846936	+	Silent	SNP	A	A	G	rs654593	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr11:100846936A>G	ENST00000298815.8	+	20	2007	c.2004A>G	c.(2002-2004)ccA>ccG	p.P668P	ARHGAP42_ENST00000524892.2_Silent_p.P634P	NM_152432.2	NP_689645.2	A6NI28	RHG42_HUMAN	Rho GTPase activating protein 42	668	Ser-rich.				signal transduction (GO:0007165)	intracellular (GO:0005622)	GTPase activator activity (GO:0005096)			endometrium(3)|skin(2)	5						TTGCAACCCCATCATCTTCCA	0.473													G|||	2874	0.573882	0.2511	0.6081	5008	,	,		20996	0.997		0.4344	False		,,,				2504	0.6933				p.P668P		Atlas-SNP	.											.	ARHGAP42	32	.	0			c.A2004G						PASS	.	G		471,913		83,305,304	54.0	43.0	46.0		2004	-7.1	0.1	11	dbSNP_83	46	1401,1781		313,775,503	no	coding-synonymous	ARHGAP42	NM_152432.2		396,1080,807	GG,GA,AA		44.0289,34.0318,40.9987		668/875	100846936	1872,2694	692	1591	2283	SO:0001819	synonymous_variant	143872	exon20			AACCCCATCATCT			11q22.1	2012-04-19			ENSG00000165895	ENSG00000165895		"""Rho GTPase activating proteins"""	26545	protein-coding gene	gene with protein product		615936				18954304	Standard	NM_152432		Approved	FLJ32810, GRAF3	uc001pge.2	A6NI28	OTTHUMG00000167530	ENST00000298815.8:c.2004A>G	11.37:g.100846936A>G		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	94	7	0.0744681	NM_152432	Q96M56	Silent	SNP	ENST00000298815.8	37																																																																																				A|0.462;G|0.538	0.538	strong		0.473	ARHGAP42-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_152432	
ZNF423	23090	hgsc.bcm.edu	37	16	49672444	49672444	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr16:49672444C>T	ENST00000561648.1	-	4	672	c.619G>A	c.(619-621)Gac>Aac	p.D207N	ZNF423_ENST00000535559.1_Missense_Mutation_p.D90N|ZNF423_ENST00000262383.2_Missense_Mutation_p.D207N|ZNF423_ENST00000567169.1_Missense_Mutation_p.D90N|ZNF423_ENST00000562871.1_Missense_Mutation_p.D147N|ZNF423_ENST00000563137.2_Missense_Mutation_p.D147N|ZNF423_ENST00000562520.1_Missense_Mutation_p.D147N	NM_001271620.1	NP_001258549.1	Q2M1K9	ZN423_HUMAN	zinc finger protein 423	207					cell differentiation (GO:0030154)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|Notch signaling pathway (GO:0007219)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.D207Y(1)		breast(1)|central_nervous_system(1)|endometrium(8)|kidney(6)|large_intestine(16)|lung(47)|ovary(1)|pancreas(2)|prostate(4)|skin(1)|urinary_tract(2)	89		all_cancers(37;0.0155)				TTGAGGTGGTCGCTGCGGGAG	0.602																																					p.D207N		Atlas-SNP	.											ZNF423_ENST00000262383,NS,carcinoma,0,1	ZNF423	463	1	1	Substitution - Missense(1)	ovary(1)	c.G619A						PASS	.						67.0	48.0	55.0					16																	49672444		2198	4300	6498	SO:0001583	missense	23090	exon4			GGTGGTCGCTGCG	AB018303	CCDS32445.1, CCDS61930.1	16q12	2014-01-28				ENSG00000102935		"""Zinc fingers, C2H2-type"""	16762	protein-coding gene	gene with protein product	"""OLF-1/EBF associated zinc finger gene"", "" Smad- and Olf-interacting zinc finger protein"", ""early B-cell factor associated zinc finger protein"""	604557				9872452, 10660046	Standard	NM_001271620		Approved	KIAA0760, OAZ, Roaz, Ebfaz, Zfp104, NPHP14, JBTS19	uc031qwd.1	Q2M1K9		ENST00000561648.1:c.619G>A	16.37:g.49672444C>T	ENSP00000455426:p.Asp207Asn	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	64	21	0.328125	NM_015069	O94860|Q76N04|Q9NZ13	Missense_Mutation	SNP	ENST00000561648.1	37	CCDS32445.1	.	.	.	.	.	.	.	.	.	.	C	20.8	4.044496	0.75732	.	.	ENSG00000102935	ENST00000262383;ENST00000535559	T;T	0.07567	3.18;3.18	5.0	5.0	0.66597	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.21881	0.0527	L	0.41079	1.255	0.49483	D	0.999796	D	0.89917	1.0	D	0.91635	0.999	T	0.01099	-1.1452	9	.	.	.	.	18.3069	0.90185	0.0:1.0:0.0:0.0	.	207	Q2M1K9	ZN423_HUMAN	N	207;90	ENSP00000262383:D207N;ENSP00000442321:D90N	.	D	-	1	0	ZNF423	48229945	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.709000	0.84645	2.331000	0.79229	0.561000	0.74099	GAC	.	.	none		0.602	ZNF423-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000423258.1	NM_015069	
NDUFAF5	79133	hgsc.bcm.edu	37	20	13779113	13779113	+	Silent	SNP	T	T	C	rs2273317	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr20:13779113T>C	ENST00000378106.5	+	6	605	c.486T>C	c.(484-486)caT>caC	p.H162H	NDUFAF5_ENST00000463598.1_Silent_p.H134H|NDUFAF5_ENST00000475968.1_3'UTR	NM_024120.4	NP_077025.2	Q5TEU4	NDUF5_HUMAN	NADH dehydrogenase (ubiquinone) complex I, assembly factor 5	162					mitochondrial respiratory chain complex I assembly (GO:0032981)	extrinsic component of mitochondrial inner membrane (GO:0031314)	methyltransferase activity (GO:0008168)	p.H162H(1)									TTAGTTTGCATTGGGTGAATG	0.308													T|||	264	0.0527157	0.0015	0.0807	5008	,	,		17672	0.1974		0.0	False		,,,				2504	0.0072				p.H162H		Atlas-SNP	.											C20orf7,NS,carcinoma,0,1	.	.	1	1	Substitution - coding silent(1)	stomach(1)	c.T486C						scavenged	.	T	,	10,4396	16.8+/-37.8	0,10,2193	153.0	150.0	151.0		402,486	-2.5	1.0	20	dbSNP_100	151	4,8594	3.0+/-9.4	0,4,4295	no	coding-synonymous,coding-synonymous	C20orf7	NM_001039375.2,NM_024120.4	,	0,14,6488	CC,CT,TT		0.0465,0.227,0.1077	,	134/318,162/346	13779113	14,12990	2203	4299	6502	SO:0001819	synonymous_variant	79133	exon6			TTTGCATTGGGTG		CCDS13118.1, CCDS33441.1	20p12.1	2012-10-12	2012-05-08	2012-05-08	ENSG00000101247	ENSG00000101247		"""Mitochondrial respiratory chain complex assembly factors"""	15899	protein-coding gene	gene with protein product		612360	"""chromosome 20 open reading frame 7"""	C20orf7		18940309, 21607760	Standard	NM_024120		Approved	dJ842G6.1	uc002wom.3	Q5TEU4	OTTHUMG00000031909	ENST00000378106.5:c.486T>C	20.37:g.13779113T>C		Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	172	6	0.0348837	NM_024120	A8K166|Q6GPH3|Q9H6F4	Silent	SNP	ENST00000378106.5	37	CCDS13118.1																																																																																			T|0.983;C|0.017	0.017	strong		0.308	NDUFAF5-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078057.2	NM_001039375	
ACOT11	26027	hgsc.bcm.edu	37	1	55064980	55064980	+	Missense_Mutation	SNP	G	G	A	rs2304303	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr1:55064980G>A	ENST00000371316.3	+	8	858	c.776G>A	c.(775-777)cGt>cAt	p.R259H	ACOT11_ENST00000343744.2_Missense_Mutation_p.R259H|ACOT11_ENST00000481208.1_3'UTR	NM_015547.3	NP_056362.1	Q8WXI4	ACO11_HUMAN	acyl-CoA thioesterase 11	259	Acyl coenzyme A hydrolase 2.				fatty acid metabolic process (GO:0006631)|intracellular signal transduction (GO:0035556)|response to cold (GO:0009409)|response to temperature stimulus (GO:0009266)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	acyl-CoA hydrolase activity (GO:0047617)|carboxylic ester hydrolase activity (GO:0052689)|lipid binding (GO:0008289)			NS(1)|central_nervous_system(1)|endometrium(6)|large_intestine(3)|lung(5)|ovary(1)	17						CGGCTCTGCCGTGCCCACCCT	0.547													G|||	404	0.0806709	0.0295	0.1412	5008	,	,		8222	0.1706		0.0348	False		,,,				2504	0.0613				p.R259H	Ovarian(148;1440 1861 22015 32453 51933)	Atlas-SNP	.											ACOT11_ENST00000371316,caecum,carcinoma,0,2	ACOT11	105	2	0			c.G776A						scavenged	.	G	HIS/ARG,HIS/ARG	153,4253	104.3+/-142.8	2,149,2052	80.0	78.0	79.0		776,776	-1.6	0.1	1	dbSNP_100	79	236,8364	95.2+/-157.0	5,226,4069	yes	missense,missense	ACOT11	NM_015547.3,NM_147161.3	29,29	7,375,6121	AA,AG,GG		2.7442,3.4725,2.9909	benign,benign	259/608,259/595	55064980	389,12617	2203	4300	6503	SO:0001583	missense	26027	exon8			TCTGCCGTGCCCA	AB014607	CCDS592.1, CCDS593.1	1p32.3	2011-09-13	2005-09-08	2005-09-08	ENSG00000162390	ENSG00000162390	3.1.2.-	"""Acyl CoA thioesterases"", ""StAR-related lipid transfer (START) domain containing"""	18156	protein-coding gene	gene with protein product	"""StAR-related lipid transfer (START) domain containing 14"""	606803	"""thioesterase, adipose associated"""	THEA		11696000, 16103133, 16940157	Standard	NM_015547		Approved	STARD14, BFIT, KIAA0707, BFIT1, THEM1	uc001cxl.2	Q8WXI4	OTTHUMG00000009891	ENST00000371316.3:c.776G>A	1.37:g.55064980G>A	ENSP00000360366:p.Arg259His	Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	182	5	0.0274725	NM_147161	B1AQ22|D3DQ50|O75187|Q52LP1|Q53ER9|Q96DI1|Q9H883	Missense_Mutation	SNP	ENST00000371316.3	37	CCDS592.1	188	0.08608058608058608	13	0.026422764227642278	48	0.13259668508287292	99	0.17307692307692307	28	0.036939313984168866	G	12.41	1.928244	0.34002	0.034725	0.027442	ENSG00000162390	ENST00000343744;ENST00000371316	T;T	0.31510	1.49;1.49	5.27	-1.58	0.08479	Thioesterase superfamily (1);	0.518159	0.21888	N	0.067627	T	0.00039	0.0001	L	0.48642	1.525	0.53688	P	2.199999999996649E-5	B;B	0.14805	0.011;0.002	B;B	0.15870	0.014;0.005	T	0.23476	-1.0187	9	0.20046	T	0.44	-9.6805	6.4701	0.22003	0.5971:0.1422:0.2607:0.0	rs2304303	259;259	Q8WXI4;Q8WXI4-2	ACO11_HUMAN;.	H	259	ENSP00000340260:R259H;ENSP00000360366:R259H	ENSP00000340260:R259H	R	+	2	0	ACOT11	54837568	0.348000	0.24861	0.096000	0.21009	0.952000	0.60782	1.950000	0.40323	-0.026000	0.13895	0.561000	0.74099	CGT	G|0.956;A|0.044	0.044	strong		0.547	ACOT11-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000027356.1	NM_015547	
RSPH3	83861	hgsc.bcm.edu	37	6	159398700	159398700	+	Missense_Mutation	SNP	C	C	T	rs3756987	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr6:159398700C>T	ENST00000252655.1	-	8	1742	c.1553G>A	c.(1552-1554)gGc>gAc	p.G518D	RSPH3_ENST00000449822.1_Missense_Mutation_p.G280D|RSPH3_ENST00000607398.1_5'Flank|RSPH3_ENST00000367069.2_Missense_Mutation_p.G376D|RSPH3_ENST00000297262.3_Missense_Mutation_p.G422D	NM_031924.4	NP_114130.3	Q86UC2	RSPH3_HUMAN	radial spoke 3 homolog (Chlamydomonas)	518			G -> D (in dbSNP:rs3756987).					p.G518D(1)		endometrium(3)|kidney(2)|large_intestine(1)|lung(7)|ovary(2)|skin(1)|stomach(7)	23		Breast(66;0.00519)|Ovarian(120;0.123)		OV - Ovarian serous cystadenocarcinoma(65;2.36e-16)|BRCA - Breast invasive adenocarcinoma(81;5.92e-06)		TTGTAGGTAGCCTCCATCTAA	0.488													T|||	1064	0.21246	0.0651	0.3746	5008	,	,		16377	0.3919		0.1034	False		,,,				2504	0.2239				p.G518D		Atlas-SNP	.											RSPH3,NS,carcinoma,0,1	RSPH3	48	1	1	Substitution - Missense(1)	stomach(1)	c.G1553A						PASS	.	T	ASP/GLY	404,4002	788.9+/-415.0	12,380,1811	198.0	185.0	190.0		1553	2.8	0.0	6	dbSNP_107	190	926,7674	777.0+/-407.7	61,804,3435	yes	missense	RSPH3	NM_031924.4	94	73,1184,5246	TT,TC,CC		10.7674,9.1693,10.226	benign	518/561	159398700	1330,11676	2203	4300	6503	SO:0001583	missense	83861	exon8			AGGTAGCCTCCAT	AF353618	CCDS5260.1	6q25.3	2014-05-16	2008-07-04	2007-06-26	ENSG00000130363	ENSG00000130363			21054	protein-coding gene	gene with protein product		615876	"""radial spokehead-like 2"""	RSHL2		12477932	Standard	NM_031924		Approved	dJ111C20.1, RSP3	uc003qrx.3	Q86UC2	OTTHUMG00000015924	ENST00000252655.1:c.1553G>A	6.37:g.159398700C>T	ENSP00000252655:p.Gly518Asp	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	92	7	0.076087	NM_031924	Q96LQ5|Q96LX2|Q9BX75	Missense_Mutation	SNP	ENST00000252655.1	37	CCDS5260.1	469	0.21474358974358973	33	0.06707317073170732	109	0.3011049723756906	244	0.42657342657342656	83	0.10949868073878628	T	0.023	-1.405423	0.01155	0.091693	0.107674	ENSG00000130363	ENST00000367069;ENST00000449822;ENST00000252655;ENST00000297262	T;T;T;T	0.10382	2.91;2.92;2.89;2.88	3.96	2.75	0.32379	.	0.930568	0.08825	N	0.888160	T	0.00695	0.0023	N	0.01168	-0.975	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.47235	-0.9133	9	0.05833	T	0.94	-0.913	3.7359	0.08510	0.1874:0.109:0.0:0.7036	rs3756987;rs59000492;rs3756987	422;518	Q86UC2-2;Q86UC2	.;RSPH3_HUMAN	D	376;280;518;422	ENSP00000356036:G376D;ENSP00000393195:G280D;ENSP00000252655:G518D;ENSP00000297262:G422D	ENSP00000252655:G518D	G	-	2	0	RSPH3	159318688	0.005000	0.15991	0.000000	0.03702	0.002000	0.02628	1.408000	0.34668	0.060000	0.16281	-0.893000	0.02921	GGC	C|0.842;T|0.158	0.158	strong		0.488	RSPH3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_031924	
UBB	7314	hgsc.bcm.edu	37	17	16285497	16285497	+	Silent	SNP	A	A	G			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr17:16285497A>G	ENST00000395837.1	+	2	457	c.276A>G	c.(274-276)gaA>gaG	p.E92E	UBB_ENST00000302182.3_Silent_p.E92E|RP11-138I1.4_ENST00000583934.1_RNA|UBB_ENST00000578649.1_Intron|UBB_ENST00000395839.1_Silent_p.E92E|UBB_ENST00000535788.1_Intron	NM_001281718.1|NM_001281720.1	NP_001268647.1|NP_001268649.1	P0CG47	UBB_HUMAN	ubiquitin B	92	Ubiquitin-like 2. {ECO:0000255|PROSITE- ProRule:PRU00214}.		GMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQ QRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFV KTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFA GKQLEDGRTLSDYNIQKESTLHLVLRLRGGC -> YADLRE DPDRQDHHPGSGAQ (in UBB(+1); loss of polyubiquitination; impairs the ubiquitin-proteasome pathway; refractory to disassembly by DUBs; slow degradation by UCHL3).		activation of MAPK activity (GO:0000187)|anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|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 peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|carbohydrate metabolic process (GO:0005975)|cellular response to hypoxia (GO:0071456)|cytokine-mediated signaling pathway (GO:0019221)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|endosomal transport (GO:0016197)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|gene expression (GO:0010467)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|innate immune response (GO:0045087)|intracellular transport of virus (GO:0075733)|ion transmembrane transport (GO:0034220)|JNK cascade (GO:0007254)|membrane organization (GO:0061024)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|negative regulation of type I interferon production (GO:0032480)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of apoptotic process (GO:0043065)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of type I interferon production (GO:0032479)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|stress-activated MAPK cascade (GO:0051403)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|transmembrane transport (GO:0055085)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral protein processing (GO:0019082)|virion assembly (GO:0019068)	cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)		p.E92E(2)		breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	16				UCEC - Uterine corpus endometrioid carcinoma (92;0.0822)		TCACCCTGGAAGTGGAGCCCA	0.557																																					p.E92E	Melanoma(163;1126 3406 34901)	Atlas-SNP	.											UBB,bladder,carcinoma,0,6	UBB	30	6	2	Substitution - coding silent(2)	endometrium(1)|central_nervous_system(1)	c.A276G						scavenged	.																																			SO:0001819	synonymous_variant	7314	exon2			CCTGGAAGTGGAG		CCDS11177.1	17p12-p11.2	2010-11-25			ENSG00000170315	ENSG00000170315			12463	protein-coding gene	gene with protein product	"""polyubiquitin B"""	191339				2154095	Standard	NM_018955		Approved	MGC8385, FLJ25987	uc002gpx.3	P0CG47	OTTHUMG00000058987	ENST00000395837.1:c.276A>G	17.37:g.16285497A>G		Somatic	198	2	0.010101		WXS	Illumina HiSeq	Phase_I	196	4	0.0204082	NM_018955	P02248|P02249|P02250|P62988|Q29120|Q6LBL4|Q6LDU5|Q8WYN8|Q91887|Q91888|Q9BWD6|Q9BX98|Q9UEF2|Q9UEG1|Q9UEK8|Q9UPK7	Silent	SNP	ENST00000395837.1	37	CCDS11177.1																																																																																			G|1.000;|0.000	1.000	weak		0.557	UBB-002	NOVEL	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000130459.1	NM_018955	
EXT2	2132	hgsc.bcm.edu	37	11	44129290	44129290	+	Silent	SNP	C	C	A	rs4755228	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr11:44129290C>A	ENST00000343631.3	+	2	157	c.28C>A	c.(28-30)Cgg>Agg	p.R10R	EXT2_ENST00000358681.4_Silent_p.R10R|EXT2_ENST00000533608.1_Silent_p.R10R|EXT2_ENST00000395673.3_Silent_p.R43R			Q93063	EXT2_HUMAN	exostosin glycosyltransferase 2	10					carbohydrate metabolic process (GO:0005975)|cell differentiation (GO:0030154)|cellular polysaccharide biosynthetic process (GO:0033692)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)|heparan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process (GO:0015014)|mesoderm formation (GO:0001707)|ossification (GO:0001503)|protein glycosylation (GO:0006486)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|intrinsic component of endoplasmic reticulum membrane (GO:0031227)|membrane (GO:0016020)	glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity (GO:0050508)|glucuronosyltransferase activity (GO:0015020)|heparan sulfate N-acetylglucosaminyltransferase activity (GO:0042328)|N-acetylglucosaminyl-proteoglycan 4-beta-glucuronosyltransferase activity (GO:0050509)|protein heterodimerization activity (GO:0046982)|transferase activity, transferring glycosyl groups (GO:0016757)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|lung(17)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	32						GTATAATATCCGGGGTCCTGC	0.483			"""Mis, N, F, S"""			"""exostoses, osteosarcoma"""			Hereditary Multiple Exostoses				C|||	391	0.0780751	0.0045	0.0519	5008	,	,		18309	0.2788		0.0089	False		,,,				2504	0.0603				p.R43R		Atlas-SNP	.	yes	Rec		Multiple Exostoses Type 2	11	11p12-p11	2132	multiple exostoses type 2 gene		M	.	EXT2	129	.	0			c.C127A						PASS	.	C	,,	37,4369	40.0+/-72.8	0,37,2166	121.0	118.0	119.0		127,28,28	4.4	1.0	11	dbSNP_111	119	39,8561	25.7+/-73.6	0,39,4261	no	coding-synonymous,coding-synonymous,coding-synonymous	EXT2	NM_000401.3,NM_001178083.1,NM_207122.1	,,	0,76,6427	AA,AC,CC		0.4535,0.8398,0.5843	,,	43/752,10/729,10/719	44129290	76,12930	2203	4300	6503	SO:0001819	synonymous_variant	2132	exon2	Familial Cancer Database	HME, Hereditary Exostoses, Multiple Osteochondromatosis, Multiple Cartilaginous Exostoses	AATATCCGGGGTC		CCDS7908.1, CCDS53618.1, CCDS53619.1	11p12-p11	2014-09-17	2013-03-01		ENSG00000151348	ENSG00000151348	2.4.1.224, 2.4.1.225	"""Exostosin glycosyltransferase family"""	3513	protein-coding gene	gene with protein product	"""Glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N- acetylglucosaminyltransferase"", ""N-acetylglucosaminyl-proteoglycan 4-beta-glucuronosyltransferase"""	608210	"""exostoses (multiple) 2"", ""exostosin 2"""			8162019, 9576285	Standard	NM_000401		Approved	SOTV	uc001mya.3	Q93063	OTTHUMG00000166498	ENST00000343631.3:c.28C>A	11.37:g.44129290C>A		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	97	4	0.0412371	NM_000401	B2R5Z6|C9JU51|J3KPT2|O15288	Silent	SNP	ENST00000343631.3	37	CCDS7908.1																																																																																			C|0.958;A|0.042	0.042	strong		0.483	EXT2-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390074.1	NM_000401	
PIGG	54872	hgsc.bcm.edu	37	4	520853	520853	+	Missense_Mutation	SNP	G	G	A	rs13114026	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr4:520853G>A	ENST00000453061.2	+	10	2201	c.2095G>A	c.(2095-2097)Gtc>Atc	p.V699I	PIGG_ENST00000296306.7_3'UTR|PIGG_ENST00000383028.4_Missense_Mutation_p.V566I|PIGG_ENST00000504346.1_Missense_Mutation_p.V610I|PIGG_ENST00000310340.5_Missense_Mutation_p.V691I	NM_001127178.1	NP_001120650.1	Q5H8A4	PIGG_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class G	699			V -> I (in dbSNP:rs13114026). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|GPI anchor biosynthetic process (GO:0006506)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	CP2 mannose-ethanolamine phosphotransferase activity (GO:0051267)|phosphotransferase activity, for other substituted phosphate groups (GO:0016780)	p.L689_A694delLSVLAA(1)		breast(1)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(5)|lung(16)|ovary(3)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	39						CGAGCTCTCTGTCCTGGCTGC	0.552													G|||	893	0.178315	0.2413	0.0908	5008	,	,		14770	0.2054		0.1292	False		,,,				2504	0.1779				p.V699I		Atlas-SNP	.											.	PIGG	86	.	1	Deletion - In frame(1)	ovary(1)	c.G2095A						PASS	.	G	ILE/VAL,ILE/VAL	1003,3403	370.8+/-319.7	117,769,1317	62.0	49.0	53.0		2095,2071	3.4	0.0	4	dbSNP_121	53	1035,7565	219.7+/-257.6	66,903,3331	yes	missense,missense	PIGG	NM_001127178.1,NM_017733.3	29,29	183,1672,4648	AA,AG,GG		12.0349,22.7644,15.6697	benign,benign	699/984,691/976	520853	2038,10968	2203	4300	6503	SO:0001583	missense	54872	exon10			CTCTCTGTCCTGG		CCDS3336.1, CCDS46992.1, CCDS75080.1, CCDS75081.1, CCDS75082.1, CCDS75083.1	4p16.3	2013-02-26	2006-06-28		ENSG00000174227	ENSG00000174227		"""Phosphatidylinositol glycan anchor biosynthesis"""	25985	protein-coding gene	gene with protein product			"""phosphatidylinositol glycan, class G"""			15632136	Standard	XM_005272287		Approved	FLJ20265, GPI7, LAS21	uc003gak.4	Q5H8A4	OTTHUMG00000112457	ENST00000453061.2:c.2095G>A	4.37:g.520853G>A	ENSP00000415203:p.Val699Ile	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	107	13	0.121495	NM_001127178	B4DKC7|Q2TAK5|Q6UX31|Q7L5Y4|Q8N866|Q8NCC9|Q96SY9|Q9BVT7|Q9NXG5	Missense_Mutation	SNP	ENST00000453061.2	37	CCDS46992.1	396	0.1813186813186813	132	0.2682926829268293	37	0.10220994475138122	130	0.22727272727272727	97	0.1279683377308707	G	2.896	-0.228623	0.06022	0.227644	0.120349	ENSG00000174227	ENST00000310340;ENST00000453061;ENST00000504346;ENST00000383028	T;T;T;T	0.09255	3.32;3.33;3.0;3.0	6.06	3.39	0.38822	.	0.669240	0.16139	N	0.227810	T	0.00012	0.0000	L	0.52011	1.625	0.58432	P	1.0000000000287557E-6	B;B;B	0.30236	0.274;0.022;0.169	B;B;B	0.30401	0.115;0.01;0.086	T	0.42932	-0.9422	9	0.12766	T	0.61	-2.4778	5.1107	0.14808	0.1524:0.0:0.5552:0.2924	rs13114026;rs59899952;rs13114026	566;699;691	Q5H8A4-3;Q5H8A4;Q5H8A4-2	.;PIGG_HUMAN;.	I	691;699;610;566	ENSP00000311750:V691I;ENSP00000415203:V699I;ENSP00000424800:V610I;ENSP00000372494:V566I	ENSP00000311750:V691I	V	+	1	0	PIGG	510853	0.063000	0.20901	0.004000	0.12327	0.216000	0.24613	0.374000	0.20501	0.437000	0.26423	-0.145000	0.13849	GTC	G|0.827;A|0.173	0.173	strong		0.552	PIGG-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000357494.1	NM_017733	
EAF2	55840	hgsc.bcm.edu	37	3	121563355	121563355	+	Silent	SNP	T	T	C	rs9884018	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr3:121563355T>C	ENST00000273668.2	+	2	233	c.162T>C	c.(160-162)ggT>ggC	p.G54G	EAF2_ENST00000451944.2_Silent_p.G54G	NM_018456.4	NP_060926.2	Q96CJ1	EAF2_HUMAN	ELL associated factor 2	54	Necessary for interaction with ELL.				apoptotic process (GO:0006915)|negative regulation of cell growth (GO:0030308)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	ELL-EAF complex (GO:0032783)|transcription elongation factor complex (GO:0008023)	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)	p.G54G(1)		endometrium(1)|kidney(2)|large_intestine(1)|lung(4)|prostate(1)	9				GBM - Glioblastoma multiforme(114;0.0972)		TTGAGGTTGGTGAAGGTGAAC	0.323													T|||	1233	0.246206	0.1339	0.1455	5008	,	,		16668	0.6161		0.1382	False		,,,				2504	0.1994				p.G54G	Esophageal Squamous(194;1942 2097 24663 29345 31866)	Atlas-SNP	.											EAF2,NS,carcinoma,0,1	EAF2	26	1	1	Substitution - coding silent(1)	prostate(1)	c.T162C						scavenged	.	T		715,3691	299.3+/-285.7	70,575,1558	125.0	129.0	128.0		162	3.3	1.0	3	dbSNP_119	128	1184,7416	241.5+/-271.8	85,1014,3201	no	coding-synonymous	EAF2	NM_018456.4		155,1589,4759	CC,CT,TT		13.7674,16.2279,14.601		54/261	121563355	1899,11107	2203	4300	6503	SO:0001819	synonymous_variant	55840	exon2			GGTTGGTGAAGGT	AF517829	CCDS3006.1	3q21.1	2007-08-01			ENSG00000145088	ENSG00000145088			23115	protein-coding gene	gene with protein product		607659				12446457, 12907652	Standard	NM_018456		Approved	BM040, TRAITS, U19	uc003een.3	Q96CJ1	OTTHUMG00000159424	ENST00000273668.2:c.162T>C	3.37:g.121563355T>C		Somatic	233	0	0		WXS	Illumina HiSeq	Phase_I	219	8	0.0365297	NM_018456	Q9NZ82	Silent	SNP	ENST00000273668.2	37	CCDS3006.1																																																																																			T|0.799;C|0.201	0.201	strong		0.323	EAF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355247.1	NM_018456	
DNAAF2	55172	hgsc.bcm.edu	37	14	50100683	50100683	+	Silent	SNP	C	C	G	rs2985686	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr14:50100683C>G	ENST00000298292.8	-	1	1265	c.1185G>C	c.(1183-1185)gcG>gcC	p.A395A	DNAAF2_ENST00000406043.3_Silent_p.A395A	NM_018139.2	NP_060609.2	Q9NVR5	KTU_HUMAN	dynein, axonemal, assembly factor 2	395					axonemal dynein complex assembly (GO:0070286)|bacterial-type flagellum-dependent cell motility (GO:0071973)|cilium-dependent cell motility (GO:0060285)|response to retinoic acid (GO:0032526)	cytoplasm (GO:0005737)				kidney(1)|lung(4)	5						CTCCGTCCTCCGCGCGACTCC	0.781													G|||	2800	0.559105	0.6702	0.6715	5008	,	,		11594	0.1736		0.7604	False		,,,				2504	0.5194				p.A395A		Atlas-SNP	.											.	DNAAF2	47	.	0			c.G1185C						PASS	.						1.0	1.0	1.0					14																	50100683		917	2082	2999	SO:0001819	synonymous_variant	55172	exon1			GTCCTCCGCGCGA	AK001425	CCDS9691.2, CCDS45100.1	14q21.3	2012-05-03	2011-06-09	2011-06-09	ENSG00000165506	ENSG00000165506			20188	protein-coding gene	gene with protein product	"""kintoun"""	612517	"""chromosome 14 open reading frame 104"""	C14orf104			Standard	NM_001083908		Approved	FLJ10563, KTU, PF13, CILD10	uc001wws.4	Q9NVR5	OTTHUMG00000152331	ENST00000298292.8:c.1185G>C	14.37:g.50100683C>G		Somatic	0	0	.		WXS	Illumina HiSeq	Phase_I	11	11	1	NM_018139	B9WS54|C0JAP7|Q86TR1|Q86TY8|Q969Z5	Silent	SNP	ENST00000298292.8	37	CCDS9691.2																																																																																			C|0.432;G|0.568	0.568	strong		0.781	DNAAF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276813.1		
CYP11B2	1585	hgsc.bcm.edu	37	8	143994041	143994041	+	Missense_Mutation	SNP	C	C	T	rs4545	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr8:143994041C>T	ENST00000323110.2	-	8	1305	c.1303G>A	c.(1303-1305)Ggc>Agc	p.G435S		NM_000498.3	NP_000489.3	P19099	C11B2_HUMAN	cytochrome P450, family 11, subfamily B, polypeptide 2	435			G -> S (in dbSNP:rs4545). {ECO:0000269|PubMed:10391209, ECO:0000269|PubMed:10391210}.		aldosterone biosynthetic process (GO:0032342)|C21-steroid hormone biosynthetic process (GO:0006700)|cellular response to hormone stimulus (GO:0032870)|cellular response to potassium ion (GO:0035865)|cortisol biosynthetic process (GO:0034651)|mineralocorticoid biosynthetic process (GO:0006705)|potassium ion homeostasis (GO:0055075)|regulation of blood volume by renal aldosterone (GO:0002017)|renal water homeostasis (GO:0003091)|small molecule metabolic process (GO:0044281)|sodium ion homeostasis (GO:0055078)|steroid metabolic process (GO:0008202)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	corticosterone 18-monooxygenase activity (GO:0047783)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|steroid 11-beta-monooxygenase activity (GO:0004507)			cervix(1)|endometrium(2)|kidney(3)|large_intestine(5)|lung(22)|ovary(3)|upper_aerodigestive_tract(3)	39	all_cancers(97;5.56e-11)|all_epithelial(106;2.49e-08)|Lung NSC(106;0.000228)|all_lung(105;0.000633)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)				Eplerenone(DB00700)|Etomidate(DB00292)|Hydrocortisone(DB00741)|Metoclopramide(DB01233)|Metyrapone(DB01011)|Spironolactone(DB00421)	AAGTTCCTGCCGGAGCCCCTG	0.622									Familial Hyperaldosteronism type I				.|||	814	0.16254	0.0295	0.1009	5008	,	,		13703	0.496		0.0229	False		,,,				2504	0.1861				p.G435S		Atlas-SNP	.											CYP11B2,NS,carcinoma,+2,1	CYP11B2	107	1	0			c.G1303A	GRCh37	CM033362	CYP11B2	M	rs4545	scavenged	.	C	SER/GLY	113,4293		3,107,2093	72.0	82.0	79.0		1303	-5.9	0.0	8	dbSNP_52	79	178,8422		6,166,4128	no	missense	CYP11B2	NM_000498.3	56	9,273,6221	TT,TC,CC		2.0698,2.5647,2.2374	benign	435/504	143994041	291,12715	2203	4300	6503	SO:0001583	missense	1585	exon8	Familial Cancer Database	Dexamethasone Sensitive Aldosteronism, FH-I	TCCTGCCGGAGCC	X54741	CCDS6393.1	8q21-q22	2013-06-19	2003-01-14		ENSG00000179142	ENSG00000179142	1.14.15.4	"""Cytochrome P450s"""	2592	protein-coding gene	gene with protein product	"""steroid 11-beta-monooxygenase"""	124080	"""cytochrome P450, subfamily XIB (steroid 11-beta-hydroxylase), polypeptide 2"""	CYP11B		1303253	Standard	NM_000498		Approved	CYP11BL, CPN2, P-450C18, P450aldo, ALDOS	uc003yxk.1	P19099	OTTHUMG00000160254	ENST00000323110.2:c.1303G>A	8.37:g.143994041C>T	ENSP00000325822:p.Gly435Ser	Somatic	153	1	0.00653595		WXS	Illumina HiSeq	Phase_I	168	3	0.0178571	NM_000498	B0ZBE4|Q16726	Missense_Mutation	SNP	ENST00000323110.2	37	CCDS6393.1	335	0.1533882783882784	14	0.028455284552845527	30	0.08287292817679558	276	0.4825174825174825	15	0.01978891820580475	.	8.410	0.843957	0.16963	0.025647	0.020698	ENSG00000179142	ENST00000323110	T	0.68331	-0.32	2.96	-5.92	0.02261	.	1.825320	0.02980	N	0.145573	T	0.00012	0.0000	L	0.42008	1.315	0.80722	P	0.0	B	0.24483	0.104	B	0.21708	0.036	T	0.24476	-1.0159	9	0.08837	T	0.75	.	7.4483	0.27223	0.0:0.2907:0.1428:0.5665	rs4545;rs57715984;rs4545	435	P19099	C11B2_HUMAN	S	435	ENSP00000325822:G435S	ENSP00000325822:G435S	G	-	1	0	CYP11B2	143991043	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.484000	0.06528	-2.274000	0.00680	-0.471000	0.05019	GGC	C|0.914;T|0.086	0.086	strong		0.622	CYP11B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359904.1		
MYO18B	84700	hgsc.bcm.edu	37	22	26164413	26164413	+	Missense_Mutation	SNP	C	C	T	rs13058434	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr22:26164413C>T	ENST00000407587.2	+	4	699	c.530C>T	c.(529-531)cCt>cTt	p.P177L	MYO18B_ENST00000536101.1_Missense_Mutation_p.P177L|MYO18B_ENST00000335473.7_Missense_Mutation_p.P177L			Q8IUG5	MY18B_HUMAN	myosin XVIIIB	177			P -> L (in dbSNP:rs13058434).			cytoplasm (GO:0005737)|nucleus (GO:0005634)|unconventional myosin complex (GO:0016461)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(2)|breast(6)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(27)|liver(2)|lung(60)|ovary(7)|prostate(8)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	146						GACGCCCCCCCTTGCAAGACC	0.597													C|||	856	0.170927	0.0242	0.1916	5008	,	,		12898	0.3026		0.0775	False		,,,				2504	0.3149				p.P177L		Atlas-SNP	.											.	MYO18B	322	.	0			c.C530T						PASS	.	C	LEU/PRO	103,3791		1,101,1845	18.0	22.0	21.0		530	3.1	0.0	22	dbSNP_121	21	639,7623		29,581,3521	yes	missense	MYO18B	NM_032608.5	98	30,682,5366	TT,TC,CC		7.7342,2.6451,6.104	benign	177/2568	26164413	742,11414	1947	4131	6078	SO:0001583	missense	84700	exon4			CCCCCCCTTGCAA	AJ310931	CCDS54507.1	22q12.1	2011-09-27			ENSG00000133454	ENSG00000133454		"""Myosins / Myosin superfamily : Class XVIII"""	18150	protein-coding gene	gene with protein product		607295				12209013, 12547197	Standard	NM_032608		Approved	BK125H2.1	uc003abz.1	Q8IUG5	OTTHUMG00000151129	ENST00000407587.2:c.530C>T	22.37:g.26164413C>T	ENSP00000386096:p.Pro177Leu	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	89	7	0.0786517	NM_032608	B2RWP3|F5GYU7|Q8NDI8|Q8TE65|Q8WWS0|Q96KH2|Q96KR8|Q96KR9	Missense_Mutation	SNP	ENST00000407587.2	37		294	0.1346153846153846	13	0.026422764227642278	59	0.16298342541436464	163	0.28496503496503495	59	0.07783641160949868	C	9.533	1.111448	0.20714	0.026451	0.077342	ENSG00000133454	ENST00000536101;ENST00000335473;ENST00000407587	D;D;D	0.86030	-2.04;-2.04;-2.06	4.14	3.08	0.35506	.	1.504210	0.04707	N	0.416900	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B;B	0.14012	0.005;0.009;0.009	B;B;B	0.09377	0.002;0.004;0.004	T	0.04005	-1.0985	9	0.32370	T	0.25	.	6.5368	0.22359	0.0:0.7141:0.1814:0.1045	rs13058434;rs56971829;rs13058434	177;177;177	Q8IUG5;F5GXR6;F5GYU7	MY18B_HUMAN;.;.	L	177	ENSP00000441229:P177L;ENSP00000334563:P177L;ENSP00000386096:P177L	ENSP00000334563:P177L	P	+	2	0	MYO18B	24494413	0.000000	0.05858	0.001000	0.08648	0.005000	0.04900	0.643000	0.24750	0.835000	0.34877	0.305000	0.20034	CCT	C|0.867;T|0.133	0.133	strong		0.597	MYO18B-006	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000400691.1	NM_032608	
CORO7	79585	hgsc.bcm.edu	37	16	4445327	4445327	+	Missense_Mutation	SNP	C	C	T	rs3747579	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr16:4445327C>T	ENST00000251166.4	-	7	723	c.578G>A	c.(577-579)cGg>cAg	p.R193Q	CORO7_ENST00000539968.1_5'UTR|CORO7-PAM16_ENST00000572467.1_Missense_Mutation_p.R193Q|CORO7_ENST00000574025.1_Missense_Mutation_p.R108Q|CORO7_ENST00000423908.2_Missense_Mutation_p.R25Q|CORO7_ENST00000537233.2_Missense_Mutation_p.R175Q	NM_024535.4	NP_078811.3	P57737	CORO7_HUMAN	coronin 7	193			R -> Q (in dbSNP:rs3747579). {ECO:0000269|PubMed:14702039}.		actin filament polymerization (GO:0030041)|Golgi to endosome transport (GO:0006895)|protein transport (GO:0015031)	cytoplasmic vesicle (GO:0031410)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|trans-Golgi network (GO:0005802)	actin binding (GO:0003779)			breast(3)|central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(8)|prostate(2)|skin(2)|urinary_tract(2)	23						GTCAAAGATCCGCAGCTGCTT	0.607													C|||	2541	0.507388	0.1172	0.5836	5008	,	,		18193	0.7817		0.7097	False		,,,				2504	0.4898				p.R193Q		Atlas-SNP	.											CORO7,NS,carcinoma,0,1	CORO7	73	1	0			c.G578A						scavenged	.	C	GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG	961,3433	363.1+/-316.4	113,735,1349	72.0	73.0	73.0		524,323,578,578	4.2	1.0	16	dbSNP_107	73	6154,2446	697.8+/-405.0	2222,1710,368	yes	missense,missense,missense,missense	CORO7,CORO7-PAM16	NM_001201472.1,NM_001201473.1,NM_001201479.1,NM_024535.4	43,43,43,43	2335,2445,1717	TT,TC,CC		28.4419,21.8707,45.244	probably-damaging,probably-damaging,probably-damaging,probably-damaging	175/908,108/841,193/1049,193/926	4445327	7115,5879	2197	4300	6497	SO:0001583	missense	79585	exon7			AAGATCCGCAGCT	AK097238	CCDS10513.1, CCDS55982.1, CCDS58417.1	16p13.3	2013-01-10			ENSG00000262246	ENSG00000262246		"""Coronins"", ""WD repeat domain containing"""	26161	protein-coding gene	gene with protein product		611668				15327992	Standard	NM_024535		Approved	FLJ22021		P57737	OTTHUMG00000129465	ENST00000251166.4:c.578G>A	16.37:g.4445327C>T	ENSP00000251166:p.Arg193Gln	Somatic	102	1	0.00980392		WXS	Illumina HiSeq	Phase_I	84	5	0.0595238	NM_024535	B4DFD6|B4DL18|I3L416|Q17RK4	Missense_Mutation	SNP	ENST00000251166.4	37	CCDS10513.1	1296	0.5934065934065934	59	0.11991869918699187	216	0.5966850828729282	471	0.8234265734265734	550	0.7255936675461742	C	17.84	3.487498	0.63962	0.218707	0.715581	ENSG00000103426	ENST00000251166;ENST00000537233;ENST00000423908	T;T	0.67865	-0.29;4.88	4.17	4.17	0.49024	WD40/YVTN repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.422202	0.23997	N	0.042517	T	0.00012	0.0000	M	0.85373	2.75	0.27201	P	0.9601589	P;D	0.71674	0.855;0.998	B;D	0.76575	0.11;0.988	T	0.38178	-0.9673	9	0.59425	D	0.04	-26.2535	11.8635	0.52480	0.0:1.0:0.0:0.0	rs3747579;rs52808084;rs56564879;rs57253852;rs3747579	108;193	P57737-2;P57737	.;CORO7_HUMAN	Q	193;108;25	ENSP00000251166:R193Q;ENSP00000391530:R25Q	ENSP00000251166:R193Q	R	-	2	0	CORO7	4385328	0.120000	0.22244	0.993000	0.49108	0.986000	0.74619	1.096000	0.30976	2.135000	0.66039	0.563000	0.77884	CGG	C|0.451;T|0.549	0.549	strong		0.607	CORO7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251628.2	NM_024535	
FRMD4A	55691	hgsc.bcm.edu	37	10	13702500	13702500	+	Missense_Mutation	SNP	G	G	A	rs145701309		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr10:13702500G>A	ENST00000357447.2	-	20	2082	c.1714C>T	c.(1714-1716)Ctc>Ttc	p.L572F	FRMD4A_ENST00000358621.4_Missense_Mutation_p.L557F|FRMD4A_ENST00000378503.1_Missense_Mutation_p.L572F	NM_018027.3	NP_060497.3	Q9P2Q2	FRM4A_HUMAN	FERM domain containing 4A	572					establishment of epithelial cell polarity (GO:0090162)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|tight junction (GO:0005923)				breast(4)|endometrium(9)|kidney(2)|large_intestine(11)|lung(9)|ovary(2)|pancreas(1)|prostate(2)|skin(1)	41						CGAGGAGGGAGTCCCTTGTGA	0.577											OREG0020030	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L572F		Atlas-SNP	.											FRMD4A,NS,carcinoma,+1,1	FRMD4A	108	1	0			c.C1714T						scavenged	.						110.0	105.0	106.0					10																	13702500		2203	4300	6503	SO:0001583	missense	55691	exon20			GAGGGAGTCCCTT	AB037715	CCDS7101.1	10p14	2004-07-15	2004-07-15	2004-07-15	ENSG00000151474	ENSG00000151474			25491	protein-coding gene	gene with protein product			"""FERM domain containing 4"""	FRMD4		10718198	Standard	NM_018027		Approved	FLJ10210, KIAA1294, bA295P9.4	uc001ims.3	Q9P2Q2	OTTHUMG00000017708	ENST00000357447.2:c.1714C>T	10.37:g.13702500G>A	ENSP00000350032:p.Leu572Phe	Somatic	126	1	0.00793651	689	WXS	Illumina HiSeq	Phase_I	149	6	0.0402685	NM_018027	A7E2Y3|Q5T377	Missense_Mutation	SNP	ENST00000357447.2	37	CCDS7101.1	.	.	.	.	.	.	.	.	.	.	G	19.09	3.759197	0.69763	.	.	ENSG00000151474	ENST00000358621;ENST00000357447;ENST00000378503	D;D;D	0.84146	-1.81;-1.81;-1.81	5.81	5.81	0.92471	.	0.000000	0.85682	D	0.000000	D	0.84942	0.5584	N	0.22421	0.69	0.80722	D	1	D	0.71674	0.998	P	0.60682	0.878	D	0.84814	0.0792	10	0.45353	T	0.12	-22.5455	13.3013	0.60326	0.0722:0.0:0.9278:0.0	.	572	Q9P2Q2	FRM4A_HUMAN	F	557;572;572	ENSP00000351438:L557F;ENSP00000350032:L572F;ENSP00000367764:L572F	ENSP00000350032:L572F	L	-	1	0	FRMD4A	13742506	1.000000	0.71417	0.998000	0.56505	0.997000	0.91878	5.616000	0.67709	2.757000	0.94681	0.462000	0.41574	CTC	G|1.000;T|0.000	.	alt		0.577	FRMD4A-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046889.1	NM_018027	
MAP3K5	4217	hgsc.bcm.edu	37	6	136944063	136944063	+	Silent	SNP	A	A	G	rs3765258	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr6:136944063A>G	ENST00000359015.4	-	15	2433	c.2073T>C	c.(2071-2073)taT>taC	p.Y691Y	MAP3K5_ENST00000355845.4_Intron	NM_005923.3	NP_005914.1	Q99683	M3K5_HUMAN	mitogen-activated protein kinase kinase kinase 5	691	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of JUN kinase activity (GO:0007257)|activation of MAPKK activity (GO:0000186)|apoptotic signaling pathway (GO:0097190)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to reactive nitrogen species (GO:1902170)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|JNK cascade (GO:0007254)|MAPK cascade (GO:0000165)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of neuron death (GO:1901216)|programmed necrotic cell death (GO:0097300)|protein phosphorylation (GO:0006468)|response to ischemia (GO:0002931)|viral process (GO:0016032)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|protein kinase complex (GO:1902911)	ATP binding (GO:0005524)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|magnesium ion binding (GO:0000287)|MAP kinase kinase kinase activity (GO:0004709)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein phosphatase binding (GO:0019903)			NS(1)|breast(1)|cervix(1)|endometrium(8)|kidney(6)|large_intestine(6)|lung(24)|ovary(2)|prostate(1)|skin(4)|urinary_tract(4)	58	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00137)|OV - Ovarian serous cystadenocarcinoma(155;0.00569)		AGACTATCCCATAAGTGCCTT	0.393													G|||	733	0.146366	0.2988	0.1326	5008	,	,		20182	0.2192		0.008	False		,,,				2504	0.0174				p.Y691Y		Atlas-SNP	.											.	MAP3K5	136	.	0			c.T2073C						PASS	.	G		1113,3293	718.8+/-408.9	135,843,1225	205.0	208.0	207.0		2073	-10.1	0.1	6	dbSNP_107	207	39,8561	817.6+/-406.9	0,39,4261	no	coding-synonymous	MAP3K5	NM_005923.3		135,882,5486	GG,GA,AA		0.4535,25.261,8.8575		691/1375	136944063	1152,11854	2203	4300	6503	SO:0001819	synonymous_variant	4217	exon15			TATCCCATAAGTG	U67156	CCDS5179.1	6q22.33	2011-06-09			ENSG00000197442	ENSG00000197442		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6857	protein-coding gene	gene with protein product	"""apoptosis signal regulating kinase 1"""	602448		MEKK5		9465908	Standard	NM_005923		Approved	MAPKKK5, ASK1	uc003qhc.3	Q99683	OTTHUMG00000015647	ENST00000359015.4:c.2073T>C	6.37:g.136944063A>G		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	60	5	0.0833333	NM_005923	A6NIA0|B4DGB2|Q5THN3|Q99461	Silent	SNP	ENST00000359015.4	37	CCDS5179.1																																																																																			A|0.870;G|0.130	0.130	strong		0.393	MAP3K5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042383.1		
PPP1R7	5510	hgsc.bcm.edu	37	2	242097275	242097275	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr2:242097275G>A	ENST00000234038.6	+	3	709	c.235G>A	c.(235-237)Gag>Aag	p.E79K	PPP1R7_ENST00000272983.8_Missense_Mutation_p.E36K|PPP1R7_ENST00000407025.1_Missense_Mutation_p.E79K|PPP1R7_ENST00000402734.1_Missense_Mutation_p.E20K|PPP1R7_ENST00000404405.3_Missense_Mutation_p.E79K|PPP1R7_ENST00000485630.1_3'UTR|PPP1R7_ENST00000401987.1_Missense_Mutation_p.E36K|PPP1R7_ENST00000406106.3_Missense_Mutation_p.E79K	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	79					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)		CAGAGATGCAGAGGTAATGCC	0.468																																					p.E79K	NSCLC(62;446 1299 5417 11238 27640)	Atlas-SNP	.											.	PPP1R7	35	.	0			c.G235A						PASS	.						83.0	73.0	76.0					2																	242097275		2203	4300	6503	SO:0001583	missense	5510	exon3			GATGCAGAGGTAA	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.235G>A	2.37:g.242097275G>A	ENSP00000234038:p.Glu79Lys	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	98	36	0.367347	NM_002712	B4DFD4|B5MCY6|Q9UQE5|Q9UQE6|Q9Y6K4	Missense_Mutation	SNP	ENST00000234038.6	37	CCDS2546.1	.	.	.	.	.	.	.	.	.	.	G	32	5.164816	0.94727	.	.	ENSG00000115685	ENST00000438799;ENST00000402734;ENST00000423280;ENST00000407025;ENST00000272983;ENST00000234038;ENST00000404405;ENST00000439916;ENST00000406106;ENST00000401987;ENST00000427172	T;T;T;T;T;T;T;T;T;T;T	0.47177	1.85;1.85;1.85;1.85;1.85;1.85;0.85;1.15;1.85;1.85;1.82	5.3	5.3	0.74995	.	0.000000	0.85682	D	0.000000	T	0.66167	0.2762	M	0.66506	2.035	0.80722	D	1	D;P;P;P;D;P	0.71674	0.996;0.947;0.902;0.893;0.998;0.956	P;P;B;P;D;P	0.80764	0.824;0.577;0.415;0.554;0.994;0.549	T	0.61917	-0.6964	10	0.27082	T	0.32	-26.0255	17.1348	0.86736	0.0:0.0:1.0:0.0	.	63;20;36;79;79;79	C9JD73;C9J177;Q15435-2;Q15435;Q15435-3;B5MBZ8	.;.;.;PP1R7_HUMAN;.;.	K	63;20;20;79;36;79;79;79;79;36;88	ENSP00000396376:E63K;ENSP00000385012:E20K;ENSP00000412092:E20K;ENSP00000385657:E79K;ENSP00000272983:E36K;ENSP00000234038:E79K;ENSP00000385498:E79K;ENSP00000409719:E79K;ENSP00000385022:E79K;ENSP00000385466:E36K;ENSP00000397985:E88K	ENSP00000234038:E79K	E	+	1	0	PPP1R7	241745948	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	8.281000	0.89905	2.490000	0.84030	0.655000	0.94253	GAG	.	.	none		0.468	PPP1R7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257244.4	NM_002712	
PNPLA7	375775	hgsc.bcm.edu	37	9	140356422	140356422	+	Silent	SNP	G	G	C	rs28452008	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr9:140356422G>C	ENST00000277531.4	-	31	3828	c.3642C>G	c.(3640-3642)ctC>ctG	p.L1214L	NSMF_ENST00000371474.3_5'Flank|PNPLA7_ENST00000492278.1_5'UTR|NSMF_ENST00000371472.2_5'Flank|NSMF_ENST00000371475.3_5'Flank|NSMF_ENST00000371473.3_5'Flank|PNPLA7_ENST00000406427.1_Silent_p.L1239L|PNPLA7_ENST00000371457.1_Silent_p.L820L|NSMF_ENST00000437259.1_5'Flank|NSMF_ENST00000265663.7_5'Flank|NSMF_ENST00000392812.4_5'Flank	NM_152286.3	NP_689499.3	Q6ZV29	PLPL7_HUMAN	patatin-like phospholipase domain containing 7	1214					lipid metabolic process (GO:0006629)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	lysophospholipase activity (GO:0004622)			breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	40	all_cancers(76;0.126)			OV - Ovarian serous cystadenocarcinoma(145;0.000268)|Epithelial(140;0.000839)		GCTGGTCGCGGAGCATCTTCT	0.706													C|||	2452	0.489617	0.3177	0.3588	5008	,	,		14382	0.8204		0.3847	False		,,,				2504	0.5818				p.L1239L		Atlas-SNP	.											PNPLA7,NS,carcinoma,0,1	PNPLA7	124	1	0			c.C3717G						PASS	.	C	,	1420,2962		231,958,1002	11.0	13.0	13.0		3717,3642	1.1	1.0	9	dbSNP_125	13	3144,5428		623,1898,1765	no	coding-synonymous,coding-synonymous	PNPLA7	NM_001098537.1,NM_152286.3	,	854,2856,2767	CC,CG,GG		36.6776,32.4053,35.2324	,	1239/1343,1214/1318	140356422	4564,8390	2191	4286	6477	SO:0001819	synonymous_variant	375775	exon32			GTCGCGGAGCATC	AK126267	CCDS7045.1, CCDS48070.1	9q34.3	2009-01-12	2006-06-12	2006-06-12	ENSG00000130653	ENSG00000130653		"""Patatin-like phospholipase domain containing"""	24768	protein-coding gene	gene with protein product		612122	"""chromosome 9 open reading frame 111"""	C9orf111		16799181, 12640454, 19029121	Standard	XM_005266082		Approved	FLJ43070, FLJ31318, FLJ44279, RP11-48C7.2, NTEL1, NTE-R1	uc010ncj.1	Q6ZV29	OTTHUMG00000020990	ENST00000277531.4:c.3642C>G	9.37:g.140356422G>C		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	78	5	0.0641026	NM_001098537	B5MDD3|Q5T364|Q658X0|Q658Y3|Q6ZTS1|Q86YU8|Q8TAY5|Q96N75|Q9H7N5	Silent	SNP	ENST00000277531.4	37	CCDS7045.1																																																																																			G|0.620;C|0.380	0.380	strong		0.706	PNPLA7-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254787.1	NM_152286	
TRPC1	7220	hgsc.bcm.edu	37	3	142503605	142503605	+	Silent	SNP	G	G	A	rs7621642	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr3:142503605G>A	ENST00000476941.1	+	7	1506	c.1020G>A	c.(1018-1020)tcG>tcA	p.S340S	TRPC1_ENST00000273482.6_Silent_p.S306S	NM_001251845.1	NP_001238774.1	P48995	TRPC1_HUMAN	transient receptor potential cation channel, subfamily C, member 1	340					axon guidance (GO:0007411)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|response to calcium ion (GO:0051592)|saliva secretion (GO:0046541)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|costamere (GO:0043034)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|sarcomere (GO:0030017)	calcium channel activity (GO:0005262)|cation channel activity (GO:0005261)|inositol 1,4,5 trisphosphate binding (GO:0070679)|ion channel binding (GO:0044325)|store-operated calcium channel activity (GO:0015279)	p.S306S(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(18)|ovary(2)|skin(2)|stomach(3)|urinary_tract(1)	37						GACAGATGTCGGGTTACCGAC	0.408													A|||	1989	0.397165	0.7602	0.1873	5008	,	,		18120	0.4077		0.2256	False		,,,				2504	0.2209				p.S340S		Atlas-SNP	.											TRPC1,NS,carcinoma,0,1	TRPC1	82	1	1	Substitution - coding silent(1)	stomach(1)	c.G1020A						scavenged	.	A		2947,1459	470.4+/-355.7	989,969,245	121.0	111.0	115.0		918	2.0	1.0	3	dbSNP_116	115	1792,6808	733.4+/-406.9	206,1380,2714	no	coding-synonymous	TRPC1	NM_003304.4		1195,2349,2959	AA,AG,GG		20.8372,33.1139,36.437		306/760	142503605	4739,8267	2203	4300	6503	SO:0001819	synonymous_variant	7220	exon7			GATGTCGGGTTAC	X89066	CCDS3126.1, CCDS58856.1	3q23	2011-12-14			ENSG00000144935	ENSG00000144935		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	12333	protein-coding gene	gene with protein product		602343				7568191, 16382100	Standard	NM_001251845		Approved	HTRP-1	uc003evc.3	P48995	OTTHUMG00000159301	ENST00000476941.1:c.1020G>A	3.37:g.142503605G>A		Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	135	3	0.0222222	NM_001251845	Q14CE4	Silent	SNP	ENST00000476941.1	37	CCDS58856.1																																																																																			G|0.616;A|0.384	0.384	strong		0.408	TRPC1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354520.1	NM_003304	
HLA-DRB5	3127	hgsc.bcm.edu	37	6	32489745	32489745	+	Missense_Mutation	SNP	C	C	G	rs41548618	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr6:32489745C>G	ENST00000374975.3	-	2	369	c.307G>C	c.(307-309)Gcg>Ccg	p.A103P		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						GTGTCCACCGCGGCGCGCCTG	0.662													C|||	1062	0.212061	0.2504	0.2291	5008	,	,		4126	0.1815		0.1928	False		,,,				2504	0.1994				p.A103P		Atlas-SNP	.											.	HLA-DRB5	31	.	0			c.G307C						PASS	.						33.0	29.0	30.0					6																	32489745		1993	3921	5914	SO:0001583	missense	3127	exon2			CCACCGCGGCGCG		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.307G>C	6.37:g.32489745C>G	ENSP00000364114:p.Ala103Pro	Somatic	0	0	.		WXS	Illumina HiSeq	Phase_I	5	5	1	NM_002125		Missense_Mutation	SNP	ENST00000374975.3	37	CCDS4751.1	.	.	.	.	.	.	.	.	.	.	.	10.96	1.497225	0.26861	.	.	ENSG00000198502	ENST00000374975	T	0.00289	8.28	4.72	-3.95	0.04118	MHC class II, alpha/beta chain, N-terminal (1);MHC class II, beta chain, N-terminal (3);MHC classes I/II-like antigen recognition protein (1);	4.343080	0.01276	N	0.009617	T	0.00300	0.0009	M	0.92970	3.365	0.80722	P	0.0	P;P	0.40681	0.719;0.727	P;P	0.59056	0.851;0.758	T	0.19943	-1.0290	9	0.54805	T	0.06	.	5.1766	0.15139	0.4567:0.3298:0.0:0.2135	rs41548618	30;103	Q29973;Q30154	.;DRB5_HUMAN	P	103	ENSP00000364114:A103P	ENSP00000364114:A103P	A	-	1	0	HLA-DRB5	32597723	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-2.552000	0.00927	-0.891000	0.03940	-3.154000	0.00058	GCG	C|0.807;G|0.193	0.193	strong		0.662	HLA-DRB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076022.2	NM_002125	
MSH3	4437	hgsc.bcm.edu	37	5	79950715	79950715	+	Missense_Mutation	SNP	G	G	C	rs144776112|rs201874762		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr5:79950715G>C	ENST00000265081.6	+	1	249	c.169G>C	c.(169-171)Gcc>Ccc	p.A57P	DHFR_ENST00000504396.1_5'Flank|DHFR_ENST00000513048.1_5'Flank|DHFR_ENST00000505337.1_5'Flank|DHFR_ENST00000511032.1_5'Flank|DHFR_ENST00000439211.2_5'UTR	NM_002439.4	NP_002430.3	P20585	MSH3_HUMAN	mutS homolog 3	57	Poly-Ala.		Missing. {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:8942985}.		ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)|maintenance of DNA repeat elements (GO:0043570)|meiotic mismatch repair (GO:0000710)|mismatch repair (GO:0006298)|negative regulation of DNA recombination (GO:0045910)|positive regulation of helicase activity (GO:0051096)|reciprocal meiotic recombination (GO:0007131)|somatic recombination of immunoglobulin gene segments (GO:0016447)	membrane (GO:0016020)|MutSbeta complex (GO:0032302)|nuclear chromosome (GO:0000228)|nucleus (GO:0005634)	ATP binding (GO:0005524)|centromeric DNA binding (GO:0019237)|damaged DNA binding (GO:0003684)|DNA-dependent ATPase activity (GO:0008094)|double-strand/single-strand DNA junction binding (GO:0000406)|enzyme binding (GO:0019899)|heteroduplex DNA loop binding (GO:0000404)|Y-form DNA binding (GO:0000403)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(12)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	29		Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244)		OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33)		ggctgcagcggccgcagcggc	0.692								Mismatch excision repair (MMR)																													p.A57P	Melanoma(88;1010 1399 13793 26548 36275)	Atlas-SNP	.											MSH3_ENST00000265081,NS,carcinoma,0,1	MSH3	129	1	0			c.G169C						PASS	.						7.0	7.0	7.0					5																	79950715		2089	4077	6166	SO:0001583	missense	4437	exon1			GCAGCGGCCGCAG	U61981	CCDS34195.1	5q11-q12	2013-09-12	2013-09-12		ENSG00000113318	ENSG00000113318			7326	protein-coding gene	gene with protein product	"""Divergent upstream protein"", ""Mismatch repair protein 1"""	600887	"""mutS (E. coli) homolog 3"", ""mutS homolog 3 (E. coli)"""				Standard	NM_002439		Approved	DUP, MRP1	uc003kgz.4	P20585	OTTHUMG00000162540	ENST00000265081.6:c.169G>C	5.37:g.79950715G>C	ENSP00000265081:p.Ala57Pro	Somatic	9	0	0		WXS	Illumina HiSeq	Phase_I	27	15	0.555556	NM_002439	A1L480|A1L482|A6NMM6|Q6PJT5|Q86UQ6|Q92867	Missense_Mutation	SNP	ENST00000265081.6	37	CCDS34195.1	362	0.16575091575091574	115	0.23373983739837398	67	0.1850828729281768	32	0.055944055944055944	148	0.19525065963060687	-	0.222	-1.028222	0.02045	.	.	ENSG00000113318	ENST00000265081	D	0.87256	-2.23	.	.	.	.	.	.	.	.	T	0.00039	0.0001	N	0.03608	-0.345	0.80722	P	0.0	.	.	.	.	.	.	T	0.02983	-1.1086	3	.	.	.	.	.	.	.	.	57	P20585	MSH3_HUMAN	P	57	ENSP00000265081:A57P	.	A	+	1	0	MSH3	79986471	0.041000	0.20044	0.049000	0.19019	0.152000	0.21847	0.000000	0.12993	0.000000	0.14550	0.000000	0.15137	GCC	G|0.835;C|0.165	0.165	strong		0.692	MSH3-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369471.1	NM_002439	
APBB1	322	hgsc.bcm.edu	37	11	6422229	6422229	+	Silent	SNP	A	A	G			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr11:6422229A>G	ENST00000609360.1	-	12	1761	c.1662T>C	c.(1660-1662)gcT>gcC	p.A554A	APBB1_ENST00000389906.2_Silent_p.A554A|APBB1_ENST00000609331.1_Silent_p.A319A|APBB1_ENST00000608704.1_Silent_p.A295A|APBB1_ENST00000530885.1_Silent_p.A332A|APBB1_ENST00000299402.6_Silent_p.A552A|APBB1_ENST00000608645.1_Silent_p.A295A|APBB1_ENST00000608655.1_Silent_p.A334A|APBB1_ENST00000529519.1_Silent_p.A79A|APBB1_ENST00000608394.1_Silent_p.A295A|APBB1_ENST00000311051.3_Silent_p.A552A	NM_001164.3	NP_001155.1	O00213	APBB1_HUMAN	amyloid beta (A4) precursor protein-binding, family B, member 1 (Fe65)	554	PID 2. {ECO:0000255|PROSITE- ProRule:PRU00148}.				apoptotic process (GO:0006915)|axonogenesis (GO:0007409)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|histone H4 acetylation (GO:0043967)|negative regulation of cell growth (GO:0030308)|negative regulation of thymidylate synthase biosynthetic process (GO:0050760)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|synapse (GO:0045202)	beta-amyloid binding (GO:0001540)|chromatin binding (GO:0003682)|histone binding (GO:0042393)|proline-rich region binding (GO:0070064)|transcription factor binding (GO:0008134)			breast(4)|endometrium(3)|kidney(1)|large_intestine(7)|lung(5)|prostate(2)|skin(1)|urinary_tract(1)	24		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;6.49e-08)|BRCA - Breast invasive adenocarcinoma(625;0.194)		CAACAGGTTTAGCAACAGGTA	0.473																																					p.A554A	GBM(147;1810 2556 5672 39622)	Atlas-SNP	.											APBB1,NS,carcinoma,-2,1	APBB1	73	1	0			c.T1662C						scavenged	.						277.0	277.0	277.0					11																	6422229		2201	4296	6497	SO:0001819	synonymous_variant	322	exon11			AGGTTTAGCAACA	L77864	CCDS31410.1, CCDS58114.1, CCDS66015.1, CCDS66016.1, CCDS66017.1, CCDS66018.1	11p15	2008-02-01				ENSG00000166313			581	protein-coding gene	gene with protein product		602709		RIR		8955346, 8894693	Standard	NM_001164		Approved	Fe65	uc001mcy.1	O00213		ENST00000609360.1:c.1662T>C	11.37:g.6422229A>G		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	179	2	0.0111732	NM_001164	A1E379|A6NH82|A6NL69|B7Z1J5|B7Z1J6|B7Z2Y0|D3DQT2|Q7Z324|Q96A93|V9GYK0|V9GYT4	Silent	SNP	ENST00000609360.1	37																																																																																				.	.	none		0.473	APBB1-023	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000471831.1	NM_001164	
TDRD5	163589	hgsc.bcm.edu	37	1	179562740	179562740	+	Missense_Mutation	SNP	G	G	C	rs61310274	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr1:179562740G>C	ENST00000367614.1	+	3	737	c.378G>C	c.(376-378)agG>agC	p.R126S	TDRD5_ENST00000294848.8_Missense_Mutation_p.R126S|RP11-545A16.4_ENST00000567150.1_RNA|TDRD5_ENST00000444136.1_Missense_Mutation_p.R126S	NM_001199091.1	NP_001186020.1	Q8NAT2	TDRD5_HUMAN	tudor domain containing 5	126				R -> S (in Ref. 3; AAI30533/AAI44059). {ECO:0000305}.	DNA methylation involved in gamete generation (GO:0043046)|P granule organization (GO:0030719)|spermatid development (GO:0007286)	chromatoid body (GO:0033391)|pi-body (GO:0071546)				NS(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(7)|lung(44)|ovary(2)|prostate(1)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)	77						ACCGAGGAAGGGTTGCCCCTA	0.453													G|||	1541	0.307708	0.0877	0.4092	5008	,	,		20589	0.371		0.3897	False		,,,				2504	0.3834				p.R126S		Atlas-SNP	.											TDRD5,NS,neuroblastoma,+1,1	TDRD5	149	1	0			c.G378C						scavenged	.	G	SER/ARG,SER/ARG,SER/ARG,SER/ARG	658,3748	279.6+/-274.9	54,550,1599	167.0	155.0	159.0		378,378,378,378	2.6	1.0	1	dbSNP_129	159	3124,5476	477.0+/-369.5	555,2014,1731	yes	missense,missense,missense,missense	TDRD5	NM_001199085.1,NM_001199089.1,NM_001199091.1,NM_173533.3	110,110,110,110	609,2564,3330	CC,CG,GG		36.3256,14.9342,29.0789	probably-damaging,probably-damaging,probably-damaging,probably-damaging	126/1036,126/1036,126/982,126/982	179562740	3782,9224	2203	4300	6503	SO:0001583	missense	163589	exon3			AGGAAGGGTTGCC	AK092142	CCDS1332.1, CCDS55663.1	1q24.2	2013-01-23			ENSG00000162782	ENSG00000162782		"""Tudor domain containing"""	20614	protein-coding gene	gene with protein product							Standard	NM_001199085		Approved	FLJ34823, TUDOR3	uc010pnp.2	Q8NAT2	OTTHUMG00000035259	ENST00000367614.1:c.378G>C	1.37:g.179562740G>C	ENSP00000356586:p.Arg126Ser	Somatic	192	1	0.00520833		WXS	Illumina HiSeq	Phase_I	260	6	0.0230769	NM_173533	A1L4G5|B7ZLV0|Q5EBN4|Q5VTV0|Q6ZSK2	Missense_Mutation	SNP	ENST00000367614.1	37	CCDS1332.1	725	0.33195970695970695	46	0.09349593495934959	153	0.42265193370165743	236	0.4125874125874126	290	0.38258575197889183	G	18.60	3.658717	0.67586	0.149342	0.363256	ENSG00000162782	ENST00000367614;ENST00000294848;ENST00000444136	T;T;T	0.12879	2.64;2.64;2.78	5.59	2.58	0.30949	.	0.200944	0.41194	D	0.000923	T	0.00012	0.0000	L	0.27053	0.805	0.31208	P	0.6990000000000001	D;D	0.89917	1.0;1.0	D;D	0.80764	0.994;0.986	T	0.46162	-0.9211	9	0.30854	T	0.27	-0.0298	7.1341	0.25519	0.3841:0.0:0.6159:0.0	rs61310274	126;126	Q8NAT2-1;Q8NAT2	.;TDRD5_HUMAN	S	126	ENSP00000356586:R126S;ENSP00000294848:R126S;ENSP00000406052:R126S	ENSP00000294848:R126S	R	+	3	2	TDRD5	177829363	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	0.835000	0.27531	0.625000	0.30304	0.655000	0.94253	AGG	G|0.693;C|0.307	0.307	strong		0.453	TDRD5-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000085295.1	NM_173533	
ANAPC1	64682	hgsc.bcm.edu	37	2	112608394	112608394	+	Missense_Mutation	SNP	T	T	C			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr2:112608394T>C	ENST00000341068.3	-	14	2381	c.1609A>G	c.(1609-1611)Act>Gct	p.T537A		NM_022662.3	NP_073153.1	Q9H1A4	APC1_HUMAN	anaphase promoting complex subunit 1	537					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)		p.T537A(5)		NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(7)|lung(16)|pancreas(1)|prostate(3)|skin(5)|stomach(1)|urinary_tract(1)	49						GGCTTTGGAGTACTAACGCCA	0.433																																					p.T537A		Atlas-SNP	.											ANAPC1,NS,carcinoma,0,9	ANAPC1	116	9	5	Substitution - Missense(5)	lung(3)|kidney(1)|endometrium(1)	c.A1609G						scavenged	.						109.0	106.0	107.0					2																	112608394		2203	4300	6503	SO:0001583	missense	64682	exon14			TTGGAGTACTAAC	AJ278357	CCDS2093.1	2q12.1	2011-06-15			ENSG00000153107	ENSG00000153107		"""Anaphase promoting complex subunits"""	19988	protein-coding gene	gene with protein product		608473				11179667	Standard	NM_022662		Approved	MCPR, TSG24, APC1	uc002ssh.3	Q9H1A4	OTTHUMG00000131277	ENST00000341068.3:c.1609A>G	2.37:g.112608394T>C	ENSP00000339109:p.Thr537Ala	Somatic	892	7	0.00784753		WXS	Illumina HiSeq	Phase_I	822	25	0.0304136	NM_022662	Q2M3H8|Q9BSE6|Q9H8D0	Missense_Mutation	SNP	ENST00000341068.3	37	CCDS2093.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	4.716|4.716	0.133071|0.133071	0.09032|0.09032	.|.	.|.	ENSG00000153107|ENSG00000153107	ENST00000341068|ENST00000427997	.|.	.|.	.|.	4.57|4.57	3.37|3.37	0.38596|0.38596	.|.	0.273018|.	0.23039|.	U|.	0.052629|.	T|T	0.55305|0.55305	0.1912|0.1912	L|L	0.45352|0.45352	1.415|1.415	0.37887|0.37887	D|D	0.930579|0.930579	B|.	0.14438|.	0.01|.	B|.	0.18263|.	0.021|.	T|T	0.53535|0.53535	-0.8425|-0.8425	9|5	0.08837|.	T|.	0.75|.	-8.0757|-8.0757	10.3103|10.3103	0.43704|0.43704	0.1479:0.0:0.0:0.8521|0.1479:0.0:0.0:0.8521	.|.	537|.	Q9H1A4|.	APC1_HUMAN|.	A|C	537|71	.|.	ENSP00000339109:T537A|.	T|Y	-|-	1|2	0|0	ANAPC1|ANAPC1	112324865|112324865	1.000000|1.000000	0.71417|0.71417	0.138000|0.138000	0.22173|0.22173	0.127000|0.127000	0.20565|0.20565	3.555000|3.555000	0.53727|0.53727	0.570000|0.570000	0.29347|0.29347	0.369000|0.369000	0.22263|0.22263	ACT|TAC	T|0.500;C|0.500	0.500	strong		0.433	ANAPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254045.2	NM_022662	
SPINK5	11005	hgsc.bcm.edu	37	5	147488367	147488367	+	Silent	SNP	C	C	T	rs2303071	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr5:147488367C>T	ENST00000256084.7	+	18	1701	c.1659C>T	c.(1657-1659)gtC>gtT	p.V553V	SPINK5_ENST00000359874.3_Silent_p.V553V|SPINK5_ENST00000398454.1_Silent_p.V553V	NM_006846.3	NP_006837.2	Q9NQ38	ISK5_HUMAN	serine peptidase inhibitor, Kazal type 5	553					anagen (GO:0042640)|epidermal cell differentiation (GO:0009913)|epithelial cell differentiation (GO:0030855)|extracellular matrix organization (GO:0030198)|hair cell differentiation (GO:0035315)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of immune response (GO:0050777)|negative regulation of proteolysis (GO:0045861)|negative regulation of serine-type peptidase activity (GO:1902572)|regulation of cell adhesion (GO:0030155)|regulation of T cell differentiation (GO:0045580)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|epidermal lamellar body (GO:0097209)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|perinuclear region of cytoplasm (GO:0048471)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.V553V(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(16)|ovary(4)|prostate(1)|skin(5)|stomach(8)|upper_aerodigestive_tract(2)	64			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			aagggaaagtcgaggctgaaa	0.373													T|||	3015	0.602037	0.8086	0.6715	5008	,	,		18248	0.4851		0.4901	False		,,,				2504	0.5092				p.V553V		Atlas-SNP	.											SPINK5_ENST00000359874,NS,carcinoma,0,3	SPINK5	245	3	1	Substitution - coding silent(1)	stomach(1)	c.C1659T						scavenged	.	T	,,	2801,869		1073,655,107	145.0	152.0	150.0		1659,1659,1659	1.4	0.0	5	dbSNP_100	150	4240,3922		1090,2060,931	no	coding-synonymous,coding-synonymous,coding-synonymous	SPINK5	NM_001127698.1,NM_001127699.1,NM_006846.3	,,	2163,2715,1038	TT,TC,CC		48.0519,23.6785,40.4919	,,	553/1095,553/917,553/1065	147488367	7041,4791	1835	4081	5916	SO:0001819	synonymous_variant	11005	exon18			GAAAGTCGAGGCT	AJ228139	CCDS43382.1, CCDS47300.1, CCDS47301.1	5q31-q32	2014-09-17	2005-08-17		ENSG00000133710	ENSG00000133710		"""Serine peptidase inhibitors, Kazal type"""	15464	protein-coding gene	gene with protein product	"""lymphoepithelial Kazal-type-related inhibitor"""	605010	"""serine protease inhibitor, Kazal type 5"""			10419450	Standard	NM_001127698		Approved	VAKTI, LEKTI, LETKI, NETS, NS, FLJ21544, FLJ97536, FLJ97596, FLJ99794, DKFZp686K19184	uc003loy.2	Q9NQ38	OTTHUMG00000134305	ENST00000256084.7:c.1659C>T	5.37:g.147488367C>T		Somatic	584	0	0		WXS	Illumina HiSeq	Phase_I	497	17	0.0342052	NM_001127699	A8MYE8|B7WPB7|D6REN5|O75770|Q3LX95|Q3LX96|Q3LX97|Q96PP2|Q96PP3	Silent	SNP	ENST00000256084.7	37	CCDS43382.1																																																																																			C|0.416;T|0.584	0.584	strong		0.373	SPINK5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000259215.2	NM_001127698	
VWA2	340706	hgsc.bcm.edu	37	10	116014769	116014769	+	Missense_Mutation	SNP	A	A	T	rs75028145	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr10:116014769A>T	ENST00000392982.3	+	4	473	c.223A>T	c.(223-225)Atc>Ttc	p.I75F	VWA2_ENST00000603594.1_Missense_Mutation_p.I75F			Q5GFL6	VWA2_HUMAN	von Willebrand factor A domain containing 2	75	VWFA 1. {ECO:0000255|PROSITE- ProRule:PRU00219}.				calcium-independent cell-matrix adhesion (GO:0007161)|protein homooligomerization (GO:0051260)|regulation of insulin receptor signaling pathway (GO:0046626)	basement membrane (GO:0005604)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	identical protein binding (GO:0042802)	p.I75F(1)		central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(6)|ovary(2)|prostate(1)|skin(1)|stomach(1)	26				Epithelial(162;0.036)|all cancers(201;0.0793)		GCACTTTGCCATCACAGTCTG	0.527													A|||	69	0.013778	0.0	0.0173	5008	,	,		20776	0.0526		0.003	False		,,,				2504	0.001				p.I75F		Atlas-SNP	.											VWA2,NS,carcinoma,0,1	VWA2	64	1	1	Substitution - Missense(1)	stomach(1)	c.A223T						scavenged	.	A	PHE/ILE	2,4404	2.1+/-5.4	0,2,2201	219.0	187.0	198.0		223	-0.4	0.9	10	dbSNP_131	198	2,8598	2.2+/-6.3	0,2,4298	yes	missense	VWA2	NM_198496.1	21	0,4,6499	TT,TA,AA		0.0233,0.0454,0.0308	possibly-damaging	75/726	116014769	4,13002	2203	4300	6503	SO:0001583	missense	340706	exon4			TTTGCCATCACAG	AK127756	CCDS7589.1, CCDS7589.2	10q25.3	2009-11-06			ENSG00000165816	ENSG00000165816			24709	protein-coding gene	gene with protein product						15580307, 14506275	Standard	NM_001272046		Approved	FLJ45857, FLJ16213, CCSP-2, AMACO, NET42	uc001lbl.2	Q5GFL6	OTTHUMG00000019082	ENST00000392982.3:c.223A>T	10.37:g.116014769A>T	ENSP00000376708:p.Ile75Phe	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	106	4	0.0377358	NM_001272046	A1A5D4|B5MDJ8|Q6ZS39|Q6ZWJ7|Q708C5|Q70UZ8	Missense_Mutation	SNP	ENST00000392982.3	37		40	0.018315018315018316	0	0.0	5	0.013812154696132596	33	0.057692307692307696	2	0.002638522427440633	A	20.5	3.995310	0.74703	4.54E-4	2.33E-4	ENSG00000165816	ENST00000392982;ENST00000298715	D	0.83591	-1.74	6.17	-0.389	0.12455	von Willebrand factor, type A (3);	1.055100	0.07318	N	0.877040	T	0.39064	0.1064	M	0.77103	2.36	0.34861	D	0.742667	P;P	0.51653	0.947;0.935	B;B	0.44044	0.439;0.401	T	0.67776	-0.5583	10	0.37606	T	0.19	.	5.0751	0.14626	0.5149:0.2686:0.2165:0.0	.	75;75	Q5GFL6;Q5GFL6-2	VWA2_HUMAN;.	F	75	ENSP00000376708:I75F	ENSP00000298715:I75F	I	+	1	0	VWA2	116004759	0.012000	0.17670	0.907000	0.35723	0.991000	0.79684	-0.575000	0.05861	-0.071000	0.12886	-0.290000	0.09829	ATC	A|0.994;T|0.006	0.006	strong		0.527	VWA2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050456.3	NM_198496	
ATG16L1	55054	hgsc.bcm.edu	37	2	234183368	234183368	+	Missense_Mutation	SNP	A	A	G	rs2241880	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr2:234183368A>G	ENST00000392017.4	+	9	1155	c.898A>G	c.(898-900)Act>Gct	p.T300A	ATG16L1_ENST00000392018.1_Missense_Mutation_p.T317A|ATG16L1_ENST00000347464.5_Missense_Mutation_p.T137A|ATG16L1_ENST00000373525.5_Missense_Mutation_p.T156A|ATG16L1_ENST00000498620.1_3'UTR|SCARNA5_ENST00000516201.1_RNA|ATG16L1_ENST00000392020.4_Missense_Mutation_p.T281A	NM_001190266.1|NM_001190267.1|NM_030803.6	NP_001177195.1|NP_001177196.1|NP_110430.5	Q676U5	A16L1_HUMAN	autophagy related 16-like 1 (S. cerevisiae)	300			T -> A (associated with susceptibility to IBD10; has no effect on the stability of the protein; enhances the cleavage and the degradation mediated by activated CASP3; results in reduced autophagy and defective clearance of intestinal pathogens; dbSNP:rs2241880). {ECO:0000269|PubMed:15620219}.		autophagic vacuole assembly (GO:0000045)|negative stranded viral RNA replication (GO:0039689)|protein homooligomerization (GO:0051260)|protein transport (GO:0015031)	autophagic vacuole (GO:0005776)|autophagic vacuole membrane (GO:0000421)|axoneme (GO:0005930)	identical protein binding (GO:0042802)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(5)|lung(7)|prostate(3)|skin(1)	25		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0179)|Acute lymphoblastic leukemia(138;0.0327)|Lung NSC(271;0.0539)		Epithelial(121;1.53e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000379)|LUSC - Lung squamous cell carcinoma(224;0.00619)|Lung(119;0.00732)|GBM - Glioblastoma multiforme(43;0.11)		CAATGTGGATACTCATCCTGG	0.473													A|||	1983	0.395966	0.3101	0.3213	5008	,	,		21225	0.3224		0.5368	False		,,,				2504	0.4959				p.T300A		Atlas-SNP	.											.	ATG16L1	83	.	0			c.A898G	GRCh37	CM070026	ATG16L1	M	rs2241880	PASS	.	A	ALA/THR,ALA/THR,ALA/THR,ALA/THR,ALA/THR	1428,2978	465.9+/-354.3	234,960,1009	181.0	149.0	160.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	646,550,841,898,409	-11.4	0.0	2	dbSNP_98	160	4506,4094	592.4+/-393.0	1198,2110,992	yes	missense,missense,missense,missense,missense	ATG16L1	NM_001190266.1,NM_001190267.1,NM_017974.3,NM_030803.6,NM_198890.2	58,58,58,58,58	1432,3070,2001	GG,GA,AA	http://www.ncbi.nlm.nih.gov/pubmed?term	47.6047,32.4103,45.6251	benign,benign,benign,benign,benign	216/524,184/492,281/589,300/608,137/445	234183368	5934,7072	2203	4300	6503	SO:0001583	missense	55054	exon9			GTGGATACTCATC	AK000897	CCDS2502.2, CCDS2503.2, CCDS54438.1	2q37.1	2014-02-12	2012-06-06	2005-09-13	ENSG00000085978	ENSG00000085978		"""WD repeat domain containing"""	21498	protein-coding gene	gene with protein product		610767	"""APG16 autophagy 16-like (S. cerevisiae)"", ""ATG16 autophagy related 16-like (S. cerevisiae)"", ""ATG16 autophagy related 16-like 1 (S. cerevisiae)"""	APG16L, ATG16L			Standard	NM_017974		Approved	WDR30, FLJ10035, ATG16A	uc002vty.3	Q676U5	OTTHUMG00000133619	ENST00000392017.4:c.898A>G	2.37:g.234183368A>G	ENSP00000375872:p.Thr300Ala	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	103	5	0.0485437	NM_030803	A3EXK9|A3EXL0|B6ZDH0|Q6IPN1|Q6UXW4|Q6ZVZ5|Q8NCY2|Q96JV5|Q9H619	Missense_Mutation	SNP	ENST00000392017.4	37	CCDS2503.2	851	0.38965201465201466	123	0.25	136	0.3756906077348066	190	0.3321678321678322	402	0.5303430079155673	A	10.98	1.504884	0.26949	0.324103	0.523953	ENSG00000085978	ENST00000392017;ENST00000347464;ENST00000444735;ENST00000373525;ENST00000419681;ENST00000392020;ENST00000392018	T;T;T;T;T;T;T	0.48522	0.88;0.92;1.09;0.99;1.71;0.81;0.91	5.71	-11.4	0.00090	WD40 repeat-like-containing domain (1);	1.946940	0.02287	N	0.069914	T	0.00012	0.0000	N	0.04203	-0.255	0.47341	P	6.049999999999667E-4	B;B;B;B;B	0.06786	0.0;0.0;0.001;0.0;0.0	B;B;B;B;B	0.10450	0.0;0.001;0.005;0.0;0.001	T	0.27536	-1.0071	9	0.14252	T	0.57	.	12.6604	0.56811	0.1798:0.4806:0.3396:0.0	rs2241880;rs17607702;rs52836811;rs57853061;rs2241880	254;281;156;300;137	B7ZLM5;Q676U5-2;Q676U5-4;Q676U5;A3EXL0	.;.;.;A16L1_HUMAN;.	A	300;137;173;156;137;281;317	ENSP00000375872:T300A;ENSP00000318259:T137A;ENSP00000409215:T173A;ENSP00000362625:T156A;ENSP00000398773:T137A;ENSP00000375875:T281A;ENSP00000375873:T317A	ENSP00000318259:T137A	T	+	1	0	ATG16L1	233848107	0.000000	0.05858	0.001000	0.08648	0.985000	0.73830	-0.395000	0.07287	-1.999000	0.00967	0.528000	0.53228	ACT	G|0.422;N|0.000	0.422	strong		0.473	ATG16L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257069.2	NM_017974	
SGTA	6449	hgsc.bcm.edu	37	19	2767594	2767594	+	Missense_Mutation	SNP	G	G	T	rs367983019		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr19:2767594G>T	ENST00000221566.2	-	3	352	c.191C>A	c.(190-192)gCg>gAg	p.A64E		NM_003021.3	NP_003012.1	O43765	SGTA_HUMAN	small glutamine-rich tetratricopeptide repeat (TPR)-containing, alpha	64					viral process (GO:0016032)	cytoplasm (GO:0005737)				endometrium(2)|large_intestine(2)|lung(2)|ovary(1)	7		Hepatocellular(1079;0.137)		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)		CGTGGCAGCCGCTTCAAATAT	0.622																																					p.A64E		Atlas-SNP	.											.	SGTA	19	.	0			c.C191A						PASS	.						42.0	37.0	39.0					19																	2767594		2203	4300	6503	SO:0001583	missense	6449	exon3			GCAGCCGCTTCAA	AJ223828	CCDS12094.1	19p13	2013-01-10	2003-11-24	2003-11-26		ENSG00000104969		"""Tetratricopeptide (TTC) repeat domain containing"""	10819	protein-coding gene	gene with protein product		603419	"""small glutamine-rich tetratricopeptide repeat (TPR)-containing"""	SGT		9740675, 12735788	Standard	NM_003021		Approved		uc002lwi.1	O43765		ENST00000221566.2:c.191C>A	19.37:g.2767594G>T	ENSP00000221566:p.Ala64Glu	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	82	4	0.0487805	NM_003021	D6W610|Q6FIA9|Q9BTZ9	Missense_Mutation	SNP	ENST00000221566.2	37	CCDS12094.1	.	.	.	.	.	.	.	.	.	.	G	1.436	-0.568915	0.03910	.	.	ENSG00000104969	ENST00000221566	T	0.35973	1.28	3.92	3.92	0.45320	.	3.510430	0.04959	U	0.461626	T	0.33469	0.0864	L	0.39245	1.2	0.35474	D	0.797628	B	0.11235	0.004	B	0.13407	0.009	T	0.15780	-1.0425	10	0.11485	T	0.65	-5.3653	13.7696	0.63018	0.0:0.0:1.0:0.0	.	64	O43765	SGTA_HUMAN	E	64	ENSP00000221566:A64E	ENSP00000221566:A64E	A	-	2	0	SGTA	2718594	0.999000	0.42202	0.930000	0.37139	0.102000	0.19082	2.917000	0.48821	1.893000	0.54813	0.491000	0.48974	GCG	.	.	alt		0.622	SGTA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451448.2	NM_003021	
PSG7	5676	hgsc.bcm.edu	37	19	43433805	43433805	+	RNA	SNP	A	A	G	rs1065178	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr19:43433805A>G	ENST00000406070.2	-	0	594				PSG7_ENST00000446844.3_RNA	NM_002783.2	NP_002774.2	Q13046	PSG7_HUMAN	pregnancy specific beta-1-glycoprotein 7 (gene/pseudogene)						female pregnancy (GO:0007565)	extracellular region (GO:0005576)							Prostate(69;0.00682)				CACAGGTTAAAATCACAGCCT	0.527													.|||	2229	0.445088	0.5666	0.4294	5008	,	,		18641	0.4216		0.2704	False		,,,				2504	0.4959				p.I44I		Atlas-SNP	.											.	.	.	.	0			c.T132C						PASS	.	G	,	2464,1938		733,998,470	220.0	217.0	218.0		132,498	-2.7	0.0	19	dbSNP_86	218	2421,6179		400,1621,2279	no	coding-synonymous,coding-synonymous	PSG7	NM_001206650.1,NM_002783.2	,	1133,2619,2749	GG,GA,AA		28.1512,44.0254,37.5711	,	44/298,166/420	43433805	4885,8117	2201	4300	6501			5676	exon2			GGTTAAAATCACA			19q13.2	2013-01-29	2010-02-26		ENSG00000221878	ENSG00000221878		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9524	protein-coding gene	gene with protein product		176396	"""pregnancy specific beta-1-glycoprotein 7"""				Standard	NM_002783		Approved		uc010xwl.2	Q13046	OTTHUMG00000151125		19.37:g.43433805A>G		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	115	5	0.0434783	NM_001206650	Q15232	Silent	SNP	ENST00000406070.2	37																																																																																				A|0.622;G|0.378	0.378	strong		0.527	PSG7-001	KNOWN	basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000321431.2	NM_001206650	
GPRC6A	222545	hgsc.bcm.edu	37	6	117113653	117113653	+	Silent	SNP	T	T	C	rs615199	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr6:117113653T>C	ENST00000310357.3	-	6	2454	c.2433A>G	c.(2431-2433)ccA>ccG	p.P811P	GPRC6A_ENST00000530250.1_Silent_p.P636P|GPRC6A_ENST00000368549.3_Silent_p.P740P	NM_148963.2	NP_683766.2	Q5T6X5	GPC6A_HUMAN	G protein-coupled receptor, class C, group 6, member A	811					calcium-mediated signaling (GO:0019722)|response to amino acid (GO:0043200)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.P811P(1)		autonomic_ganglia(1)|breast(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(8)|liver(1)|lung(24)|ovary(5)|pancreas(1)|skin(5)|stomach(3)|upper_aerodigestive_tract(3)	65		all_cancers(87;0.0314)|all_epithelial(87;0.0216)|Colorectal(196;0.234)		GBM - Glioblastoma multiforme(226;0.0265)|all cancers(137;0.0554)|OV - Ovarian serous cystadenocarcinoma(136;0.07)		TCTCCACAGCTGGTACATATT	0.343													T|||	1534	0.30631	0.1452	0.3674	5008	,	,		24347	0.5228		0.3082	False		,,,				2504	0.2556				p.P811P		Atlas-SNP	.											GPRC6A,NS,carcinoma,0,1	GPRC6A	152	1	1	Substitution - coding silent(1)	stomach(1)	c.A2433G						PASS	.	T		744,3662	304.1+/-288.3	65,614,1524	79.0	81.0	81.0		2433	-5.8	0.3	6	dbSNP_83	81	2838,5762	446.6+/-361.3	459,1920,1921	no	coding-synonymous	GPRC6A	NM_148963.2		524,2534,3445	CC,CT,TT		33.0,16.8861,27.5411		811/927	117113653	3582,9424	2203	4300	6503	SO:0001819	synonymous_variant	222545	exon6			CACAGCTGGTACA	AF502962	CCDS5112.1, CCDS69184.1, CCDS69185.1	6q22.31	2014-01-30	2014-01-30		ENSG00000173612	ENSG00000173612		"""GPCR / Class C : Calcium-sensing receptors"""	18510	protein-coding gene	gene with protein product			"""G protein-coupled receptor, family C, group 6, member A"""				Standard	NM_001286354		Approved	bA86F4.3	uc003pxj.1	Q5T6X5	OTTHUMG00000015447	ENST00000310357.3:c.2433A>G	6.37:g.117113653T>C		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	79	5	0.0632911	NM_148963	Q6JK43|Q6JK44|Q8NGU8|Q8NHZ9|Q8TDT6	Silent	SNP	ENST00000310357.3	37	CCDS5112.1																																																																																			C|0.301;N|0.000	0.301	strong		0.343	GPRC6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041966.2		
DNAH10	196385	hgsc.bcm.edu	37	12	124274474	124274474	+	Splice_Site	SNP	A	A	G	rs10846559	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr12:124274474A>G	ENST00000409039.3	+	11	1463	c.1438A>G	c.(1438-1440)Att>Gtt	p.I480V		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	480	Stem. {ECO:0000250}.		I -> V (in dbSNP:rs10846559). {ECO:0000269|PubMed:14702039}.		microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)		GATTGGACAGATTTTGGAGGA	0.443													G|||	4196	0.837859	0.8775	0.7738	5008	,	,		18865	0.998		0.7127	False		,,,				2504	0.7935				p.I480V		Atlas-SNP	.											.	DNAH10	888	.	0			c.A1438G						PASS	.	G	VAL/ILE	3743,663	281.1+/-275.7	1587,569,47	71.0	75.0	74.0		1438	5.2	1.0	12	dbSNP_120	74	5759,2841	447.5+/-361.5	1955,1849,496	yes	missense-near-splice	DNAH10	NM_207437.3	29	3542,2418,543	GG,GA,AA		33.0349,15.0477,26.9414	benign	480/4472	124274474	9502,3504	2203	4300	6503	SO:0001630	splice_region_variant	196385	exon11			GGACAGATTTTGG	AJ132089	CCDS9255.2	12q24	2008-02-05	2006-09-04		ENSG00000197653	ENSG00000197653		"""Axonemal dyneins"""	2941	protein-coding gene	gene with protein product		605884	"""dynein, axonemal, heavy polypeptide 10"""				Standard	NM_207437		Approved	FLJ43808	uc001uft.4	Q8IVF4	OTTHUMG00000154477	ENST00000409039.3:c.1438-1A>G	12.37:g.124274474A>G		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	118	10	0.0847458	NM_207437	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Missense_Mutation	SNP	ENST00000409039.3	37	CCDS9255.2	1809	0.8282967032967034	421	0.8556910569105691	283	0.7817679558011049	571	0.9982517482517482	534	0.7044854881266491	G	0.183	-1.060517	0.01950	0.849523	0.669651	ENSG00000197653	ENST00000409039	T	0.55052	0.54	5.2	5.2	0.72013	Dynein heavy chain, domain-1 (1);	0.410436	0.20194	N	0.097259	T	0.00012	0.0000	N	0.00185	-1.9	0.50313	P	1.3900000000000023E-4	B	0.02656	0.0	B	0.04013	0.001	T	0.39683	-0.9602	8	.	.	.	.	12.3487	0.55136	0.079:0.0:0.921:0.0	rs10846559;rs58161138;rs10846559	480	Q8IVF4	DYH10_HUMAN	V	480	ENSP00000386770:I480V	.	I	+	1	0	DNAH10	122840427	1.000000	0.71417	0.973000	0.42090	0.431000	0.31685	3.354000	0.52254	1.222000	0.43521	-0.222000	0.12452	ATT	A|0.235;G|0.765	0.765	strong		0.443	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3		Missense_Mutation
OR6B1	135946	hgsc.bcm.edu	37	7	143701884	143701884	+	Silent	SNP	C	C	T	rs728275	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr7:143701884C>T	ENST00000408922.2	+	1	863	c.795C>T	c.(793-795)gcC>gcT	p.A265A		NM_001005281.1	NP_001005281.1	O95007	OR6B1_HUMAN	olfactory receptor, family 6, subfamily B, member 1	265						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(3)|large_intestine(3)|lung(15)|ovary(2)|skin(2)|urinary_tract(1)	27	Melanoma(164;0.0783)					TTATCCATGCCTTCAACATGA	0.428													C|||	1939	0.387181	0.3381	0.5461	5008	,	,		23941	0.5823		0.3201	False		,,,				2504	0.2086				p.A265A		Atlas-SNP	.											.	OR6B1	60	.	0			c.C795T						PASS	.	C		1274,2644		199,876,884	138.0	129.0	132.0		795	2.4	1.0	7	dbSNP_86	132	2979,5325		542,1895,1715	no	coding-synonymous	OR6B1	NM_001005281.1		741,2771,2599	TT,TC,CC		35.8743,32.5166,34.7979		265/312	143701884	4253,7969	1959	4152	6111	SO:0001819	synonymous_variant	135946	exon1			CCATGCCTTCAAC		CCDS43667.1	7q33-q35	2012-08-09			ENSG00000221813	ENSG00000221813		"""GPCR / Class A : Olfactory receptors"""	8354	protein-coding gene	gene with protein product							Standard	NM_001005281		Approved	OR7-3	uc003wdt.1	O95007	OTTHUMG00000157765	ENST00000408922.2:c.795C>T	7.37:g.143701884C>T		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	73	4	0.0547945	NM_001005281	A4D2G2|B9EH47|Q6IFP6|Q96R38	Silent	SNP	ENST00000408922.2	37	CCDS43667.1																																																																																			C|0.586;T|0.414	0.414	strong		0.428	OR6B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349566.1		
ABCC5	10057	hgsc.bcm.edu	37	3	183699516	183699516	+	Splice_Site	SNP	T	T	C	rs7636910	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr3:183699516T>C	ENST00000334444.6	-	8	1386	c.1146A>G	c.(1144-1146)caA>caG	p.Q382Q	ABCC5_ENST00000492216.1_5'UTR|ABCC5_ENST00000265586.6_Splice_Site_p.Q382Q	NM_005688.2	NP_005679.2	O15440	MRP5_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 5	382	ABC transmembrane type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan biosynthetic process (GO:0030213)|hyaluronan metabolic process (GO:0030212)|organic anion transport (GO:0015711)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|organic anion transmembrane transporter activity (GO:0008514)	p.Q382Q(1)		NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(32)|ovary(3)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	62	all_cancers(143;1.85e-10)|Ovarian(172;0.0303)		Epithelial(37;1.74e-35)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)		Adefovir Dipivoxil(DB00718)|Alprostadil(DB00770)|Atorvastatin(DB01076)|Cisplatin(DB00515)|Dinoprostone(DB00917)|Dipyridamole(DB00975)|Fluorouracil(DB00544)|Glutathione(DB00143)|Mercaptopurine(DB01033)|Probenecid(DB01032)|Rifampicin(DB01045)|Sildenafil(DB00203)|Sulfinpyrazone(DB01138)|Zidovudine(DB00495)	TAAACTCACTTTGAACACTCT	0.378													T|||	1674	0.334265	0.2224	0.2925	5008	,	,		20737	0.4167		0.3867	False		,,,				2504	0.3763				p.Q382Q		Atlas-SNP	.											ABCC5,NS,carcinoma,0,1	ABCC5	142	1	1	Substitution - coding silent(1)	stomach(1)	c.A1146G						scavenged	.	T		1026,2724		144,738,993	96.0	94.0	94.0		1146	4.6	1.0	3	dbSNP_116	94	3065,5149		562,1941,1604	yes	coding-synonymous-near-splice	ABCC5	NM_005688.2		706,2679,2597	CC,CT,TT		37.3143,27.36,34.1942		382/1438	183699516	4091,7873	1875	4107	5982	SO:0001630	splice_region_variant	10057	exon8			CTCACTTTGAACA	AF104942	CCDS33898.1, CCDS43176.1	3q27	2012-03-14			ENSG00000114770	ENSG00000114770		"""ATP binding cassette transporters / subfamily C"""	56	protein-coding gene	gene with protein product		605251				8894702, 9827529	Standard	XM_005247058		Approved	MRP5, SMRP, EST277145, MOAT-C	uc003fmg.3	O15440	OTTHUMG00000156871	ENST00000334444.6:c.1147+1A>G	3.37:g.183699516T>C		Somatic	179	1	0.00558659		WXS	Illumina HiSeq	Phase_I	193	9	0.0466321	NM_005688	B9EIQ2|O14517|Q29ZA9|Q29ZB1|Q86UX3|Q86W30|Q9UN85|Q9UNP5|Q9UQC3	Silent	SNP	ENST00000334444.6	37	CCDS43176.1																																																																																			T|0.657;C|0.343	0.343	strong		0.378	ABCC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346350.1	NM_005688	Silent
DOCK5	80005	hgsc.bcm.edu	37	8	25222165	25222165	+	Missense_Mutation	SNP	A	A	G	rs2271111	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr8:25222165A>G	ENST00000276440.7	+	30	3112	c.3068A>G	c.(3067-3069)cAg>cGg	p.Q1023R		NM_024940.6	NP_079216.4	Q9H7D0	DOCK5_HUMAN	dedicator of cytokinesis 5	1023			Q -> R (in dbSNP:rs2271111).		positive regulation of GTPase activity (GO:0043547)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	guanyl-nucleotide exchange factor activity (GO:0005085)	p.Q1023R(1)		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)		GCTATAAATCAGTTTGCTGAA	0.418													A|||	1230	0.245607	0.0711	0.304	5008	,	,		18344	0.3562		0.3698	False		,,,				2504	0.1984				p.Q1023R	Pancreas(145;34 1887 3271 10937 30165)	Atlas-SNP	.											DOCK5,NS,carcinoma,0,1	DOCK5	167	1	1	Substitution - Missense(1)	stomach(1)	c.A3068G						scavenged	.	A	ARG/GLN	487,3919	213.8+/-233.3	26,435,1742	137.0	117.0	124.0		3068	4.3	1.0	8	dbSNP_100	124	2886,5714	414.1+/-351.3	498,1890,1912	yes	missense	DOCK5	NM_024940.6	43	524,2325,3654	GG,GA,AA		33.5581,11.0531,25.9342	benign	1023/1871	25222165	3373,9633	2203	4300	6503	SO:0001583	missense	80005	exon30			TAAATCAGTTTGC		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.3068A>G	8.37:g.25222165A>G	ENSP00000276440:p.Gln1023Arg	Somatic	212	0	0		WXS	Illumina HiSeq	Phase_I	187	6	0.0320856	NM_024940	B2RNY0|Q5XKD5|Q6AI11|Q6PJS6|Q6ZTS6	Missense_Mutation	SNP	ENST00000276440.7	37	CCDS6047.1	634	0.2902930402930403	37	0.07520325203252033	120	0.3314917127071823	189	0.3304195804195804	288	0.37994722955145116	A	10.21	1.287145	0.23478	0.110531	0.335581	ENSG00000147459	ENST00000276440	T	0.23950	1.88	5.62	4.34	0.51931	.	0.058883	0.64402	D	0.000001	T	0.00012	0.0000	L	0.41710	1.295	0.23920	P	0.99646016	B;B	0.06786	0.001;0.001	B;B	0.10450	0.005;0.005	T	0.41858	-0.9485	9	0.08837	T	0.75	.	7.572	0.27913	0.7907:0.0:0.073:0.1362	rs2271111;rs52835832;rs58353884;rs2271111	1013;1023	D3DSS6;Q9H7D0	.;DOCK5_HUMAN	R	1023	ENSP00000276440:Q1023R	ENSP00000276440:Q1023R	Q	+	2	0	DOCK5	25278082	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	4.300000	0.59079	2.142000	0.66516	0.528000	0.53228	CAG	A|0.749;G|0.251	0.251	strong		0.418	DOCK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254955.2	NM_024940	
WDR60	55112	hgsc.bcm.edu	37	7	158672619	158672619	+	Missense_Mutation	SNP	A	A	G	rs2788478	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr7:158672619A>G	ENST00000407559.3	+	5	976	c.818A>G	c.(817-819)cAa>cGa	p.Q273R		NM_018051.4	NP_060521.4	Q8WVS4	WDR60_HUMAN	WD repeat domain 60	273			Q -> R (in dbSNP:rs2788478).		cell projection organization (GO:0030030)	cilium (GO:0005929)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				NS(3)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(3)|kidney(1)|large_intestine(2)|liver(4)|lung(16)|ovary(2)	35	Ovarian(565;0.152)	all_cancers(7;1.25e-09)|all_epithelial(9;0.000894)|all_hematologic(28;0.00603)	OV - Ovarian serous cystadenocarcinoma(82;0.00174)	UCEC - Uterine corpus endometrioid carcinoma (81;0.19)|STAD - Stomach adenocarcinoma(7;0.18)		GAGAGGCACCAAAGCAACGTG	0.438													G|||	2873	0.573682	0.7368	0.4294	5008	,	,		19248	0.7212		0.3837	False		,,,				2504	0.499				p.Q273R		Atlas-SNP	.											.	WDR60	94	.	0			c.A818G						PASS	.		ARG/GLN	2463,1307		809,845,231	73.0	77.0	76.0		818	0.8	0.0	7	dbSNP_100	76	3004,5188		552,1900,1644	yes	missense	WDR60	NM_018051.4	43	1361,2745,1875	GG,GA,AA		36.6699,34.6684,45.7031	benign	273/1067	158672619	5467,6495	1885	4096	5981	SO:0001583	missense	55112	exon5			GGCACCAAAGCAA		CCDS47757.1	7q36.3	2013-11-15			ENSG00000126870	ENSG00000126870		"""WD repeat domain containing"""	21862	protein-coding gene	gene with protein product		615462				23910462	Standard	NM_018051		Approved	FLJ10300, FAP163	uc003woe.4	Q8WVS4	OTTHUMG00000151443	ENST00000407559.3:c.818A>G	7.37:g.158672619A>G	ENSP00000384290:p.Gln273Arg	Somatic	253	0	0		WXS	Illumina HiSeq	Phase_I	252	14	0.0555556	NM_018051	Q9NW58	Missense_Mutation	SNP	ENST00000407559.3	37	CCDS47757.1	1191	0.5453296703296703	354	0.7195121951219512	155	0.4281767955801105	394	0.6888111888111889	288	0.37994722955145116	G	0.033	-1.322301	0.01320	0.653316	0.366699	ENSG00000126870	ENST00000407559	T	0.18016	2.24	4.73	0.795	0.18643	.	0.669254	0.12904	N	0.429496	T	0.00012	0.0000	N	0.02539	-0.55	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.36841	-0.9731	9	0.02654	T	1	0.3405	5.0153	0.14333	0.3597:0.1489:0.4914:0.0	rs2788478;rs9654723;rs10349453;rs52836646;rs56855193;rs2788478	273	Q8WVS4	WDR60_HUMAN	R	273	ENSP00000384290:Q273R	ENSP00000384290:Q273R	Q	+	2	0	WDR60	158365380	0.000000	0.05858	0.004000	0.12327	0.000000	0.00434	0.042000	0.13949	-0.043000	0.13513	-0.726000	0.03593	CAA	A|0.435;G|0.565	0.565	strong		0.438	WDR60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322668.1	NM_018051	
SLC16A4	9122	hgsc.bcm.edu	37	1	110924353	110924353	+	Silent	SNP	G	G	A	rs3738750	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr1:110924353G>A	ENST00000369779.4	-	4	534	c.285C>T	c.(283-285)ttC>ttT	p.F95F	SLC16A4_ENST00000497687.1_Intron|SLC16A4_ENST00000541986.1_Silent_p.F33F|SLC16A4_ENST00000437429.2_Intron|LAMTOR5-AS1_ENST00000590413.1_RNA|SLC16A4_ENST00000369781.4_Silent_p.F95F|SLC16A4_ENST00000472422.2_Intron	NM_001201547.1|NM_004696.2	NP_001188476.1|NP_004687.1	O15374	MOT5_HUMAN	solute carrier family 16, member 4	95					monocarboxylic acid transport (GO:0015718)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	monocarboxylic acid transmembrane transporter activity (GO:0008028)|symporter activity (GO:0015293)	p.F95F(1)		breast(1)|endometrium(1)|kidney(4)|large_intestine(2)|lung(2)|ovary(3)|prostate(1)|stomach(2)	16		all_cancers(81;0.000476)|all_epithelial(167;0.000401)|all_lung(203;0.00277)|Lung NSC(277;0.0043)		Lung(183;0.0251)|all cancers(265;0.0766)|Epithelial(280;0.0807)|Colorectal(144;0.112)|LUSC - Lung squamous cell carcinoma(189;0.14)	Pyruvic acid(DB00119)	CAGTAACAACGAAAGCCCCAA	0.418													G|||	881	0.175919	0.0318	0.1614	5008	,	,		20217	0.2609		0.1889	False		,,,				2504	0.2802				p.F95F		Atlas-SNP	.											SLC16A4,NS,carcinoma,0,2	SLC16A4	47	2	1	Substitution - coding silent(1)	stomach(1)	c.C285T						scavenged	.	G	,,,,	245,4161	145.0+/-179.8	6,233,1964	111.0	102.0	105.0		,99,,285,285	0.8	0.0	1	dbSNP_107	105	1593,7007	297.9+/-303.7	135,1323,2842	no	intron,coding-synonymous,intron,coding-synonymous,coding-synonymous	SLC16A4	NM_001201546.1,NM_001201547.1,NM_001201548.1,NM_001201549.1,NM_004696.2	,,,,	141,1556,4806	AA,AG,GG		18.5233,5.5606,14.1319	,,,,	,33/426,,95/320,95/488	110924353	1838,11168	2203	4300	6503	SO:0001819	synonymous_variant	9122	exon4			AACAACGAAAGCC	U59185	CCDS823.1, CCDS55621.1, CCDS55622.1, CCDS55623.1, CCDS55624.1	1p13.3	2013-07-18	2013-07-18		ENSG00000168679	ENSG00000168679		"""Solute carriers"""	10925	protein-coding gene	gene with protein product		603878	"""solute carrier family 16 (monocarboxylic acid transporters), member 4"", ""solute carrier family 16, member 4 (monocarboxylic acid transporter 5)"""			9425115	Standard	NM_004696		Approved	MCT4, MCT5	uc001dzo.2	O15374	OTTHUMG00000011285	ENST00000369779.4:c.285C>T	1.37:g.110924353G>A		Somatic	441	1	0.00226757		WXS	Illumina HiSeq	Phase_I	448	8	0.0178571	NM_004696	A8K3V5|B2R9C9|B4DJ67|B4DPX7|E7EPY8|G3V175|Q5T612|Q8WU09	Silent	SNP	ENST00000369779.4	37	CCDS823.1																																																																																			G|0.839;A|0.161	0.161	strong		0.418	SLC16A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000031115.3	NM_004696	
PLCE1	51196	hgsc.bcm.edu	37	10	95791613	95791613	+	Silent	SNP	T	T	C	rs17109671	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr10:95791613T>C	ENST00000371380.3	+	1	1045	c.810T>C	c.(808-810)tgT>tgC	p.C270C	PLCE1_ENST00000260766.3_Silent_p.C270C			Q9P212	PLCE1_HUMAN	phospholipase C, epsilon 1	270					activation of MAPK activity (GO:0000187)|calcium-mediated signaling (GO:0019722)|cell proliferation (GO:0008283)|cytoskeleton organization (GO:0007010)|diacylglycerol biosynthetic process (GO:0006651)|epidermal growth factor receptor signaling pathway (GO:0007173)|glomerulus development (GO:0032835)|heart development (GO:0007507)|inositol phosphate metabolic process (GO:0043647)|inositol phosphate-mediated signaling (GO:0048016)|lipid catabolic process (GO:0016042)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|phospholipid metabolic process (GO:0006644)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of GTPase activity (GO:0043547)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|Ras protein signal transduction (GO:0007265)|regulation of cell growth (GO:0001558)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|regulation of protein kinase activity (GO:0045859)|regulation of Ras protein signal transduction (GO:0046578)|regulation of smooth muscle contraction (GO:0006940)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|enzyme binding (GO:0019899)|guanyl-nucleotide exchange factor activity (GO:0005085)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|Ras GTPase binding (GO:0017016)|receptor signaling protein activity (GO:0005057)			liver(1)|ovary(2)|skin(4)|upper_aerodigestive_tract(1)	8		Colorectal(252;0.0458)				AAGGCTCTTGTGAGAAGGTTG	0.393													C|||	2306	0.460463	0.7799	0.2608	5008	,	,		20815	0.4792		0.3032	False		,,,				2504	0.3129				p.C270C		Atlas-SNP	.											PLCE1_ENST00000260766,colon,carcinoma,0,2	PLCE1	543	2	0			c.T810C						scavenged	.	C		2599,1237		883,833,202	127.0	122.0	124.0		810	3.1	0.7	10	dbSNP_123	124	2192,6054		286,1620,2217	no	coding-synonymous	PLCE1	NM_016341.3		1169,2453,2419	CC,CT,TT		26.5826,32.2471,39.654		270/2303	95791613	4791,7291	1918	4123	6041	SO:0001819	synonymous_variant	51196	exon2			CTCTTGTGAGAAG		CCDS41552.1, CCDS53555.1	10q23	2010-02-22			ENSG00000138193	ENSG00000138193	3.1.4.11		17175	protein-coding gene	gene with protein product	"""nephrosis type 3"""	608414				11022047, 11022048	Standard	NM_016341		Approved	KIAA1516, PLCE, NPHS3	uc001kjk.3	Q9P212	OTTHUMG00000018789	ENST00000371380.3:c.810T>C	10.37:g.95791613T>C		Somatic	195	0	0		WXS	Illumina HiSeq	Phase_I	169	4	0.0236686	NM_016341	A6NGW0|A6NLA1|A7MBN7|A8K1D7|B9EIJ6|Q1X6H8|Q5VWL4|Q5VWL5|Q9H9X8|Q9HBX6|Q9HC53|Q9UHV3	Silent	SNP	ENST00000371380.3	37	CCDS41552.1																																																																																			T|0.609;C|0.391	0.391	strong		0.393	PLCE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049469.3	NM_016341	
ZNF860	344787	hgsc.bcm.edu	37	3	32031622	32031622	+	Missense_Mutation	SNP	T	T	C	rs13087612	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr3:32031622T>C	ENST00000360311.4	+	2	1600	c.1051T>C	c.(1051-1053)Ttc>Ctc	p.F351L		NM_001137674.2	NP_001131146.2	A6NHJ4	ZN860_HUMAN	zinc finger protein 860	351					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(3)|lung(4)|ovary(1)	8						TGAAAAGGCTTTCAGGCGTGA	0.398													T|||	2329	0.465056	0.7799	0.3573	5008	,	,		21477	0.4524		0.1968	False		,,,				2504	0.4049				p.F351L		Atlas-SNP	.											ZNF860_ENST00000360311,NS,carcinoma,0,2	ZNF860	96	2	0			c.T1051C						scavenged	.	T	LEU/PHE	897,487		298,301,93	48.0	49.0	49.0		1051	0.3	0.0	3	dbSNP_121	49	608,2574		57,494,1040	yes	missense	ZNF860	NM_001137674.2	22	355,795,1133	CC,CT,TT		19.1075,35.1879,32.961	probably-damaging	351/633	32031622	1505,3061	692	1591	2283	SO:0001583	missense	344787	exon2			AAGGCTTTCAGGC	AK294003	CCDS46784.1	3p24.1	2013-01-08			ENSG00000197385	ENSG00000197385		"""Zinc fingers, C2H2-type"", ""-"""	34513	protein-coding gene	gene with protein product							Standard	NM_001137674		Approved		uc011axg.2	A6NHJ4	OTTHUMG00000155838	ENST00000360311.4:c.1051T>C	3.37:g.32031622T>C	ENSP00000373274:p.Phe351Leu	Somatic	345	1	0.00289855		WXS	Illumina HiSeq	Phase_I	346	4	0.0115607	NM_001137674	B4DFA4	Missense_Mutation	SNP	ENST00000360311.4	37	CCDS46784.1	899	0.4116300366300366	373	0.758130081300813	125	0.3453038674033149	248	0.43356643356643354	153	0.20184696569920843	T	14.79	2.640073	0.47153	0.648121	0.191075	ENSG00000197385	ENST00000360311	T	0.46063	0.88	0.345	0.345	0.16011	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	M	0.90977	3.165	0.58432	P	5.999999999950489E-6	D	0.63880	0.993	D	0.68192	0.956	T	0.39683	-0.9602	7	.	.	.	.	4.9959	0.14240	0.0:2.0E-4:0.0:0.9998	rs13087612;rs59979195;rs13087612	351	A6NHJ4	ZN860_HUMAN	L	351	ENSP00000373274:F351L	.	F	+	1	0	ZNF860	32006626	0.979000	0.34478	0.003000	0.11579	0.003000	0.03518	5.394000	0.66285	0.332000	0.23536	0.323000	0.21402	TTC	T|0.621;C|0.379	0.379	strong		0.398	ZNF860-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341957.1		
ACTR8	93973	hgsc.bcm.edu	37	3	53905308	53905308	+	Silent	SNP	T	T	C	rs1046677	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr3:53905308T>C	ENST00000335754.3	-	11	1618	c.1518A>G	c.(1516-1518)ggA>ggG	p.G506G	ACTR8_ENST00000488802.1_5'Flank|ACTR8_ENST00000482349.1_Silent_p.G395G|ACTR8_ENST00000231909.7_Silent_p.G211G	NM_022899.4	NP_075050.3	Q9H981	ARP8_HUMAN	ARP8 actin-related protein 8 homolog (yeast)	506					chromatin remodeling (GO:0006338)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|mitotic nuclear division (GO:0007067)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	Ino80 complex (GO:0031011)|nucleus (GO:0005634)	ATP binding (GO:0005524)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(6)|ovary(2)|prostate(1)	19				BRCA - Breast invasive adenocarcinoma(193;0.000143)|KIRC - Kidney renal clear cell carcinoma(284;0.00544)|Kidney(284;0.00607)|OV - Ovarian serous cystadenocarcinoma(275;0.111)		CCAGGGCTTTTCCTTCAAACA	0.547													C|||	3467	0.692292	0.7186	0.6196	5008	,	,		19990	0.9444		0.4523	False		,,,				2504	0.6953				p.G506G		Atlas-SNP	.											ACTR8_ENST00000231909,NS,carcinoma,-2,2	ACTR8	56	2	0			c.A1518G						scavenged	.	C		2977,1429	464.5+/-353.9	1009,959,235	103.0	100.0	101.0		1518	-2.5	0.9	3	dbSNP_86	101	3771,4829	614.9+/-396.3	814,2143,1343	no	coding-synonymous	ACTR8	NM_022899.4		1823,3102,1578	CC,CT,TT		43.8488,32.433,48.1163		506/625	53905308	6748,6258	2203	4300	6503	SO:0001819	synonymous_variant	93973	exon11			GGCTTTTCCTTCA		CCDS2875.1	3p21.31	2011-07-06	2001-11-28		ENSG00000113812	ENSG00000113812		"""INO80 complex subunits"""	14672	protein-coding gene	gene with protein product	"""INO80 complex subunit N"""		"""ARP8 (actin-related protein 8, yeast) homolog"""			18163988, 16230350	Standard	NM_022899		Approved	INO80N	uc003dhd.3	Q9H981	OTTHUMG00000158279	ENST00000335754.3:c.1518A>G	3.37:g.53905308T>C		Somatic	155	1	0.00645161		WXS	Illumina HiSeq	Phase_I	136	5	0.0367647	NM_022899	B3KSW7|Q8N566|Q9H663	Silent	SNP	ENST00000335754.3	37	CCDS2875.1	1456	0.6666666666666666	363	0.7378048780487805	223	0.6160220994475138	541	0.9458041958041958	329	0.4340369393139842	C	9.636	1.137708	0.21123	0.67567	0.438488	ENSG00000113812	ENST00000486794	.	.	.	5.67	-2.54	0.06307	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999996	.	.	.	.	.	.	T	0.19976	-1.0289	3	.	.	.	-11.7537	7.8427	0.29408	0.0:0.2982:0.3936:0.3082	rs1046677;rs17641862;rs17846012;rs17858996;rs57230247;rs1046677	.	.	.	G	260	.	.	E	-	2	0	ACTR8	53880348	0.916000	0.31088	0.936000	0.37596	0.958000	0.62258	-0.016000	0.12613	-0.796000	0.04456	-1.551000	0.00897	GAA	T|0.410;C|0.590	0.590	strong		0.547	ACTR8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350562.2	NM_022899	
CFH	3075	hgsc.bcm.edu	37	1	196695742	196695742	+	Silent	SNP	A	A	G	rs3753396	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr1:196695742A>G	ENST00000367429.4	+	13	2256	c.2016A>G	c.(2014-2016)caA>caG	p.Q672Q		NM_000186.3	NP_000177.2	P08603	CFAH_HUMAN	complement factor H	672	Sushi 11. {ECO:0000255|PROSITE- ProRule:PRU00302}.				complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	heparan sulfate proteoglycan binding (GO:0043395)|heparin binding (GO:0008201)			NS(3)|breast(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(24)|lung(33)|ovary(1)|prostate(5)|skin(9)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	101						ATAAAATTCAATGTGTTGATG	0.299													A|||	1016	0.202875	0.0378	0.1916	5008	,	,		15851	0.5099		0.1759	False		,,,				2504	0.1452				p.Q672Q		Atlas-SNP	.											CFH,NS,carcinoma,+2,3	CFH	251	3	0			c.A2016G	GRCh37	CM033783	CFH	M	rs3753396	scavenged	.	A		293,4113	159.2+/-191.8	10,273,1920	95.0	98.0	97.0		2016	-2.2	0.9	1	dbSNP_107	97	1488,7112	281.7+/-295.2	140,1208,2952	no	coding-synonymous	CFH	NM_000186.3		150,1481,4872	GG,GA,AA		17.3023,6.65,13.6937		672/1232	196695742	1781,11225	2203	4300	6503	SO:0001819	synonymous_variant	3075	exon13			AATTCAATGTGTT	Y00716	CCDS1385.1	1q32	2014-09-17	2004-08-09	2004-08-12	ENSG00000000971	ENSG00000000971		"""Complement system"""	4883	protein-coding gene	gene with protein product	"""beta-1H"", ""H factor 2 (complement)"", ""age-related maculopathy susceptibility 1"""	134370	"""H factor 1 (complement)"""	HF, HF1, HF2		2889480, 2963625	Standard	NM_000186		Approved	HUS, FHL1, ARMS1, ARMD4	uc001gtj.4	P08603	OTTHUMG00000035607	ENST00000367429.4:c.2016A>G	1.37:g.196695742A>G		Somatic	441	1	0.00226757		WXS	Illumina HiSeq	Phase_I	570	6	0.0105263	NM_000186	A5PL14|P78435|Q14570|Q2TAZ5|Q38G77|Q5TFM3|Q8N708|Q9NU86	Silent	SNP	ENST00000367429.4	37	CCDS1385.1																																																																																			A|0.777;G|0.223	0.223	strong		0.299	CFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086412.2	NM_000186	
IFNA21	3452	hgsc.bcm.edu	37	9	21166246	21166246	+	Silent	SNP	G	G	A	rs139462830		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr9:21166246G>A	ENST00000380225.1	-	1	413	c.366C>T	c.(364-366)tgC>tgT	p.C122C		NM_002175.2	NP_002166.2	P01568	IFN21_HUMAN	interferon, alpha 21	122					adaptive immune response (GO:0002250)|B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|humoral immune response (GO:0006959)|innate immune response (GO:0045087)|natural killer cell activation involved in immune response (GO:0002323)|positive regulation of peptidyl-serine phosphorylation of STAT protein (GO:0033141)|regulation of MHC class I biosynthetic process (GO:0045343)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to exogenous dsRNA (GO:0043330)|T cell activation involved in immune response (GO:0002286)|type I interferon signaling pathway (GO:0060337)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	cytokine activity (GO:0005125)|cytokine receptor binding (GO:0005126)|type I interferon receptor binding (GO:0005132)			NS(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(5)|skin(3)	14				GBM - Glioblastoma multiforme(5;1.93e-187)|Lung(24;2.12e-22)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)		CCTGTATCACGCAGGCTTCCA	0.468																																					p.C122C		Atlas-SNP	.											IFNA21,colon,carcinoma,0,1	IFNA21	25	1	0			c.C366T						scavenged	.	G		2,4404		0,2,2201	169.0	175.0	173.0		366	-1.1	0.0	9	dbSNP_134	173	0,8600		0,0,4300	no	coding-synonymous	IFNA21	NM_002175.2		0,2,6501	AA,AG,GG		0.0,0.0454,0.0154		122/190	21166246	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	3452	exon1			TATCACGCAGGCT		CCDS6497.1	9p22	2010-12-10			ENSG00000137080	ENSG00000137080		"""Interferons"""	5424	protein-coding gene	gene with protein product	"""leukocyte interferon protein"""	147584				1385305	Standard	NM_002175		Approved	IFN-alphaI	uc003zom.2	P01568	OTTHUMG00000019653	ENST00000380225.1:c.366C>T	9.37:g.21166246G>A		Somatic	244	0	0		WXS	Illumina HiSeq	Phase_I	241	4	0.0165975	NM_002175	Q14608|Q5VWD1|Q7M4Q4	Silent	SNP	ENST00000380225.1	37	CCDS6497.1																																																																																			G|1.000;A|0.000	0.000	weak		0.468	IFNA21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051882.1	NM_002175	
PHC2	1912	hgsc.bcm.edu	37	1	33820033	33820033	+	Silent	SNP	C	C	T	rs16835408	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr1:33820033C>T	ENST00000257118.5	-	8	1577	c.1524G>A	c.(1522-1524)acG>acA	p.T508T	PHC2_ENST00000373422.3_Silent_p.T114T|PHC2_ENST00000431992.1_Silent_p.T479T|PHC2_ENST00000373416.1_5'UTR|RP11-415J8.5_ENST00000432703.1_RNA|PHC2_ENST00000419414.2_Silent_p.T509T	NM_198040.2	NP_932157.1	Q8IXK0	PHC2_HUMAN	polyhomeotic homolog 2 (Drosophila)	508					multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	heterochromatin (GO:0000792)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|liver(1)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	31		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.211)				TGTTAGGGCTCGTGGGTACAG	0.612													C|||	587	0.117212	0.0083	0.072	5008	,	,		19208	0.2927		0.1183	False		,,,				2504	0.1145				p.T508T		Atlas-SNP	.											.	PHC2	78	.	0			c.G1524A						PASS	.	C		122,4284	92.0+/-130.7	2,118,2083	102.0	91.0	95.0		1524	4.6	1.0	1	dbSNP_123	95	1025,7575	218.7+/-257.0	61,903,3336	no	coding-synonymous	PHC2	NM_198040.2		63,1021,5419	TT,TC,CC		11.9186,2.769,8.819		508/859	33820033	1147,11859	2203	4300	6503	SO:0001819	synonymous_variant	1912	exon8			AGGGCTCGTGGGT	AJ419231	CCDS378.1, CCDS379.1	1p34.3	2013-01-10	2006-09-12	2002-11-15	ENSG00000134686	ENSG00000134686		"""Sterile alpha motif (SAM) domain containing"""	3183	protein-coding gene	gene with protein product		602979	"""early development regulator 2 (homolog of polyhomeotic 2)"", ""polyhomeotic-like 2 (Drosophila)"""	EDR2		9121482, 12384788	Standard	NM_198040		Approved	HPH2	uc001bxg.1	Q8IXK0	OTTHUMG00000004133	ENST00000257118.5:c.1524G>A	1.37:g.33820033C>T		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	76	6	0.0789474	NM_198040	A1L4Q1|A8KA40|D3DPR2|Q2TAL3|Q5T0C1|Q6NUJ6|Q6ZQR1|Q8N306|Q8TAG8|Q96BL4|Q9Y4Y7	Silent	SNP	ENST00000257118.5	37	CCDS378.1																																																																																			C|0.900;T|0.100	0.100	strong		0.612	PHC2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000011895.1	NM_198040	
CD3D	915	hgsc.bcm.edu	37	11	118211113	118211113	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr11:118211113G>A	ENST00000300692.4	-	2	387	c.251C>T	c.(250-252)tCt>tTt	p.S84F	CD3D_ENST00000392884.2_Missense_Mutation_p.S84F|CD3D_ENST00000529594.1_Intron	NM_000732.4	NP_000723.1	P04234	CD3D_HUMAN	CD3d molecule, delta (CD3-TCR complex)	84					cell surface receptor signaling pathway (GO:0007166)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive thymic T cell selection (GO:0045059)|regulation of immune response (GO:0050776)|T cell costimulation (GO:0031295)|T cell differentiation (GO:0030217)|T cell receptor signaling pathway (GO:0050852)	alpha-beta T cell receptor complex (GO:0042105)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|T cell receptor complex (GO:0042101)	protein heterodimerization activity (GO:0046982)|transcription coactivator activity (GO:0003713)|transmembrane signaling receptor activity (GO:0004888)			large_intestine(1)|lung(4)|ovary(1)|prostate(1)|skin(2)	9	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)	TTGCACGGTAGATTCTTTGTC	0.458																																					p.S84F		Atlas-SNP	.											.	CD3D	21	.	0			c.C251T						PASS	.						224.0	173.0	191.0					11																	118211113		2200	4296	6496	SO:0001583	missense	915	exon2			ACGGTAGATTCTT	X01451	CCDS8394.1, CCDS41724.1	11q23	2014-09-17	2006-03-28		ENSG00000167286	ENSG00000167286		"""CD molecules"""	1673	protein-coding gene	gene with protein product		186790	"""CD3d antigen, delta polypeptide (TiT3 complex)"""	T3D			Standard	NM_000732		Approved		uc001pss.1	P04234	OTTHUMG00000166970	ENST00000300692.4:c.251C>T	11.37:g.118211113G>A	ENSP00000300692:p.Ser84Phe	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	102	25	0.245098	NM_000732	A8MVP6	Missense_Mutation	SNP	ENST00000300692.4	37	CCDS8394.1	.	.	.	.	.	.	.	.	.	.	G	11.19	1.566084	0.27915	.	.	ENSG00000167286	ENST00000300692;ENST00000392884	T;T	0.49720	2.09;0.77	5.15	-0.336	0.12658	Immunoglobulin-like fold (1);	1.180960	0.05785	N	0.609330	T	0.38054	0.1026	L	0.59436	1.845	0.09310	N	1	B;B	0.12630	0.006;0.006	B;B	0.08055	0.003;0.003	T	0.19745	-1.0296	10	0.10111	T	0.7	3.1627	4.787	0.13230	0.171:0.0:0.3239:0.5051	.	84;84	A8MVP6;P04234	.;CD3D_HUMAN	F	84	ENSP00000300692:S84F;ENSP00000376622:S84F	ENSP00000300692:S84F	S	-	2	0	CD3D	117716323	0.000000	0.05858	0.000000	0.03702	0.410000	0.31052	-0.767000	0.04720	-0.223000	0.09943	0.655000	0.94253	TCT	.	.	none		0.458	CD3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392128.1	NM_000732	
NRAP	4892	hgsc.bcm.edu	37	10	115377290	115377290	+	Missense_Mutation	SNP	T	T	C	rs77678145	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr10:115377290T>C	ENST00000359988.3	-	26	3141	c.2897A>G	c.(2896-2898)gAt>gGt	p.D966G	NRAP_ENST00000369360.3_Missense_Mutation_p.D939G|NRAP_ENST00000360478.3_Missense_Mutation_p.D931G|NRAP_ENST00000369358.4_Missense_Mutation_p.D974G	NM_001261463.1|NM_198060.3	NP_001248392.1|NP_932326.2			nebulin-related anchoring protein											autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(18)|lung(39)|ovary(6)|prostate(3)|skin(1)|stomach(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	95		Colorectal(252;0.0233)|Breast(234;0.188)		Epithelial(162;0.00392)|all cancers(201;0.00569)		CTTCAAAGCATCTGGATGCTG	0.388													T|||	351	0.0700879	0.0008	0.0677	5008	,	,		19691	0.1528		0.0825	False		,,,				2504	0.0675				p.D966G		Atlas-SNP	.											.	NRAP	208	.	0			c.A2897G						PASS	.	T	GLY/ASP,GLY/ASP	80,4326	69.8+/-107.6	1,78,2124	143.0	137.0	139.0		2792,2897	4.9	1.0	10	dbSNP_131	139	751,7849	180.3+/-229.3	37,677,3586	yes	missense,missense	NRAP	NM_006175.3,NM_198060.2	94,94	38,755,5710	CC,CT,TT		8.7326,1.8157,6.3894	benign,benign	931/1696,966/1731	115377290	831,12175	2203	4300	6503	SO:0001583	missense	4892	exon26			AAAGCATCTGGAT		CCDS7578.1, CCDS7579.1, CCDS73199.1	10q24-q26	2008-08-01			ENSG00000197893	ENSG00000197893			7988	protein-coding gene	gene with protein product		602873				12789664, 10320340	Standard	NM_006175		Approved		uc001lal.4	Q86VF7	OTTHUMG00000019072	ENST00000359988.3:c.2897A>G	10.37:g.115377290T>C	ENSP00000353078:p.Asp966Gly	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	75	4	0.0533333	NM_001261463		Missense_Mutation	SNP	ENST00000359988.3	37	CCDS7579.1	154	0.07051282051282051	2	0.0040650406504065045	24	0.06629834254143646	65	0.11363636363636363	63	0.08311345646437995	T	13.95	2.390625	0.42410	0.018157	0.087326	ENSG00000197893	ENST00000369358;ENST00000369360;ENST00000359988;ENST00000360478	T;T;T;T	0.18174	2.43;2.46;2.32;2.23	6.17	4.86	0.63082	.	0.251467	0.48286	D	0.000187	T	0.00328	0.0010	L	0.43152	1.355	0.33783	P	0.375452	B;B;B	0.25719	0.081;0.132;0.007	B;B;B	0.32624	0.071;0.149;0.011	T	0.07121	-1.0789	9	0.48119	T	0.1	.	8.7616	0.34678	0.0:0.0729:0.1303:0.7969	.	966;931;966	A0AVL2;Q86VF7-4;Q86VF7	.;.;NRAP_HUMAN	G	974;939;966;931	ENSP00000358365:D974G;ENSP00000358367:D939G;ENSP00000353078:D966G;ENSP00000353666:D931G	ENSP00000353078:D966G	D	-	2	0	NRAP	115367280	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	0.967000	0.29344	2.371000	0.80710	0.533000	0.62120	GAT	A|0.000;C|0.068;T|0.932	0.068	strong		0.388	NRAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050425.2	NM_006175	
OR6M1	390261	hgsc.bcm.edu	37	11	123676690	123676690	+	Missense_Mutation	SNP	G	G	T			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr11:123676690G>T	ENST00000309154.2	-	1	405	c.368C>A	c.(367-369)gCt>gAt	p.A123D		NM_001005325.1	NP_001005325.1	Q8NGM8	OR6M1_HUMAN	olfactory receptor, family 6, subfamily M, member 1	123						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(13)|prostate(2)|skin(5)|urinary_tract(1)	29		Breast(109;0.0109)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.028)		GTCGCAGATAGCCATGTAGCG	0.507																																					p.A123D		Atlas-SNP	.											.	OR6M1	60	.	0			c.C368A						PASS	.						51.0	52.0	52.0					11																	123676690		2202	4299	6501	SO:0001583	missense	390261	exon1			CAGATAGCCATGT	AB065762	CCDS31696.1	11q24.1	2012-08-09			ENSG00000196099	ENSG00000196099		"""GPCR / Class A : Olfactory receptors"""	14711	protein-coding gene	gene with protein product							Standard	NM_001005325		Approved		uc010rzz.2	Q8NGM8	OTTHUMG00000166012	ENST00000309154.2:c.368C>A	11.37:g.123676690G>T	ENSP00000311038:p.Ala123Asp	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	97	36	0.371134	NM_001005325	B2RNK0|Q6IEW9|Q96R37	Missense_Mutation	SNP	ENST00000309154.2	37	CCDS31696.1	.	.	.	.	.	.	.	.	.	.	G	16.13	3.035627	0.54896	.	.	ENSG00000196099	ENST00000309154	T	0.01234	5.13	3.68	2.73	0.32206	GPCR, rhodopsin-like superfamily (1);	0.000000	0.33127	U	0.005259	T	0.13114	0.0318	H	0.98133	4.155	0.35910	D	0.831017	D	0.89917	1.0	D	0.80764	0.994	T	0.14392	-1.0474	10	0.87932	D	0	.	9.2511	0.37555	0.1145:0.0:0.8855:0.0	.	123	Q8NGM8	OR6M1_HUMAN	D	123	ENSP00000311038:A123D	ENSP00000311038:A123D	A	-	2	0	OR6M1	123181900	1.000000	0.71417	1.000000	0.80357	0.398000	0.30690	6.085000	0.71343	1.862000	0.54008	0.655000	0.94253	GCT	.	.	none		0.507	OR6M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387437.1	NM_001005325	
MUC4	4585	hgsc.bcm.edu	37	3	195510156	195510156	+	Missense_Mutation	SNP	G	G	C	rs201141296	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr3:195510156G>C	ENST00000463781.3	-	2	8754	c.8295C>G	c.(8293-8295)caC>caG	p.H2765Q	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.H2765Q	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.H2765H(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)		GAGGGGTGGCGTGACCTGTGG	0.572																																					p.H2765Q		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,4	MUC4	1505	4	1	Substitution - coding silent(1)	prostate(1)	c.C8295G						scavenged	.						28.0	17.0	21.0					3																	195510156		686	1527	2213	SO:0001583	missense	4585	exon2			GGTGGCGTGACCT	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.8295C>G	3.37:g.195510156G>C	ENSP00000417498:p.His2765Gln	Somatic	43	4	0.0930233		WXS	Illumina HiSeq	Phase_I	45	5	0.111111	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	.	.	.	.	.	.	.	.	.	.	-	9.079	0.998914	0.19121	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.26957	1.7;1.74	1.02	1.02	0.19986	.	.	.	.	.	T	0.10594	0.0259	N	0.19112	0.55	0.09310	N	1	P	0.45212	0.853	B	0.26693	0.072	T	0.17837	-1.0356	8	.	.	.	.	7.5733	0.27920	0.0:0.0:1.0:0.0	.	2637	E7ESK3	.	Q	2765	ENSP00000417498:H2765Q;ENSP00000420243:H2765Q	.	H	-	3	2	MUC4	196994935	0.000000	0.05858	0.010000	0.14722	0.124000	0.20399	0.020000	0.13466	0.489000	0.27749	0.074000	0.15403	CAC	G|0.996;A|0.004	.	alt		0.572	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
PEX26	55670	hgsc.bcm.edu	37	22	18562701	18562701	+	Missense_Mutation	SNP	C	C	T	rs62641228		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr22:18562701C>T	ENST00000329627.7	+	3	498	c.292C>T	c.(292-294)Cgg>Tgg	p.R98W	XXbac-B476C20.9_ENST00000607927.1_RNA|PEX26_ENST00000428061.2_Missense_Mutation_p.R98W|PEX26_ENST00000399744.3_Missense_Mutation_p.R98W|XXbac-B476C20.9_ENST00000426483.1_RNA	NM_017929.5	NP_060399.1	Q7Z412	PEX26_HUMAN	peroxisomal biogenesis factor 26	98			R -> W (in PBD7B; neonatal adrenoleukodystrophy; affects the interaction with PEX6). {ECO:0000269|PubMed:12717447, ECO:0000269|PubMed:12851857}.		protein import into peroxisome matrix (GO:0016558)|protein import into peroxisome membrane (GO:0045046)	integral component of peroxisomal membrane (GO:0005779)|peroxisome (GO:0005777)	ATPase binding (GO:0051117)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)	p.R98W(1)		breast(1)|kidney(2)|large_intestine(3)|lung(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13						AGAAATGGATCGGTGGCAAGA	0.517																																					p.R98W		Atlas-SNP	.											PEX26,NS,carcinoma,0,1	PEX26	27	1	1	Substitution - Missense(1)	lung(1)	c.C292T	GRCh37	CM032027	PEX26	M	rs62641228	scavenged	.	C	TRP/ARG,TRP/ARG,TRP/ARG	0,4406		0,0,2203	159.0	139.0	146.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	292,292,292	5.5	1.0	22	dbSNP_129	146	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense,missense	PEX26	NM_001127649.2,NM_001199319.1,NM_017929.5	101,101,101	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging	98/306,98/257,98/306	18562701	1,13005	2203	4300	6503	SO:0001583	missense	55670	exon2			ATGGATCGGTGGC	AB089678	CCDS13750.1, CCDS56221.1	22q11.21	2008-08-26	2008-08-26		ENSG00000215193	ENSG00000215193			22965	protein-coding gene	gene with protein product		608666	"""peroxisome biogenesis factor 26"""			12717447, 12851857	Standard	NM_017929		Approved	FLJ20695	uc002znp.4	Q7Z412	OTTHUMG00000149970	ENST00000329627.7:c.292C>T	22.37:g.18562701C>T	ENSP00000331106:p.Arg98Trp	Somatic	244	0	0		WXS	Illumina HiSeq	Phase_I	187	4	0.0213904	NM_001127649	F6UBB5|Q7Z413|Q7Z414|Q7Z415|Q7Z416|Q96B12|Q9NWQ0|Q9NXU0	Missense_Mutation	SNP	ENST00000329627.7	37	CCDS13750.1	.	.	.	.	.	.	.	.	.	.	C	27.2	4.812586	0.90707	0.0	1.16E-4	ENSG00000215193	ENST00000329627;ENST00000399744;ENST00000428061;ENST00000399746	D;D;D	0.94793	-3.52;-3.52;-3.52	5.46	5.46	0.80206	.	0.207499	0.33057	U	0.005321	D	0.97114	0.9057	M	0.78637	2.42	0.47698	A	0.999494	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.97461	1.0034	9	0.87932	D	0	-20.661	16.8283	0.85937	0.0:1.0:0.0:0.0	rs62641228	98;98	F6UBB5;Q7Z412	.;PEX26_HUMAN	W	98	ENSP00000331106:R98W;ENSP00000382648:R98W;ENSP00000412441:R98W	ENSP00000331106:R98W	R	+	1	2	PEX26	16942701	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	6.630000	0.74272	2.724000	0.93272	0.491000	0.48974	CGG	C|1.000;T|0.000	0.000	weak		0.517	PEX26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314644.3	NM_017929	
KIAA1551	55196	hgsc.bcm.edu	37	12	32134926	32134926	+	Missense_Mutation	SNP	G	G	A	rs3207618	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr12:32134926G>A	ENST00000312561.4	+	4	1451	c.1037G>A	c.(1036-1038)aGc>aAc	p.S346N	KIAA1551_ENST00000535596.1_Intron	NM_018169.3	NP_060639	Q9HCM1	K1551_HUMAN	KIAA1551	346			S -> N (in dbSNP:rs3207618).														AATACCAACAGCAAACAGCCT	0.373													G|||	325	0.0648962	0.0113	0.0519	5008	,	,		21302	0.0387		0.0974	False		,,,				2504	0.1401				p.S346N		Atlas-SNP	.											.	.	.	.	0			c.G1037A						PASS	.	G	ASN/SER	100,4306	81.9+/-120.4	0,100,2103	86.0	85.0	85.0		1037	-4.9	0.0	12	dbSNP_105	85	776,7824	183.9+/-232.0	36,704,3560	yes	missense	C12orf35	NM_018169.3	46	36,804,5663	AA,AG,GG		9.0233,2.2696,6.7354	possibly-damaging	346/1748	32134926	876,12130	2203	4300	6503	SO:0001583	missense	55196	exon4			CCAACAGCAAACA	AK001514	CCDS8725.2	12p11.21	2012-08-14	2012-08-14	2012-08-14	ENSG00000174718	ENSG00000174718			25559	protein-coding gene	gene with protein product			"""chromosome 12 open reading frame 35"""	C12orf35		10997877	Standard	NM_018169		Approved	FLJ20696, FLJ10652	uc001rks.3	Q9HCM1	OTTHUMG00000128501	ENST00000312561.4:c.1037G>A	12.37:g.32134926G>A	ENSP00000310338:p.Ser346Asn	Somatic	190	0	0		WXS	Illumina HiSeq	Phase_I	237	10	0.0421941	NM_018169	B2RTU5|Q4KN17|Q9NVL6|Q9NWP9	Missense_Mutation	SNP	ENST00000312561.4	37	CCDS8725.2	129	0.059065934065934064	10	0.02032520325203252	22	0.06077348066298342	25	0.043706293706293704	72	0.09498680738786279	G	11.74	1.728058	0.30593	0.022696	0.090233	ENSG00000174718	ENST00000312561;ENST00000381054	T;T	0.05855	4.01;3.38	4.83	-4.92	0.03075	.	1.697680	0.03571	N	0.228670	T	0.00144	0.0004	N	0.14661	0.345	0.09310	N	1	B	0.21688	0.059	B	0.21917	0.037	T	0.41197	-0.9522	9	.	.	.	.	0.7298	0.00955	0.298:0.2423:0.2947:0.1649	rs3207618;rs57271607;rs3207618	346	Q9HCM1	CL035_HUMAN	N	346	ENSP00000310338:S346N;ENSP00000370442:S346N	.	S	+	2	0	C12orf35	32026193	0.000000	0.05858	0.000000	0.03702	0.015000	0.08874	-0.552000	0.06020	-0.838000	0.04218	-0.410000	0.06199	AGC	G|0.936;A|0.064	0.064	strong		0.373	KIAA1551-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250307.2	NM_018169	
POM121	9883	hgsc.bcm.edu	37	7	72413423	72413423	+	Missense_Mutation	SNP	C	C	T	rs71554686	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr7:72413423C>T	ENST00000434423.2	+	11	2891	c.2891C>T	c.(2890-2892)cCg>cTg	p.P964L	POM121_ENST00000358357.3_Missense_Mutation_p.P699L|POM121_ENST00000257622.4_Missense_Mutation_p.P699L|POM121_ENST00000395270.1_Missense_Mutation_p.P699L|POM121_ENST00000446813.1_Missense_Mutation_p.P699L			Q96HA1	P121A_HUMAN	POM121 transmembrane nucleoporin	964	Pore side. {ECO:0000255}.				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)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)		p.P699L(1)		NS(1)|breast(1)|endometrium(9)|kidney(4)|large_intestine(6)|lung(12)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	41		Lung NSC(55;0.163)				CCATCATATCCGGGAGCCAAC	0.647																																					p.P699L		Atlas-SNP	.											POM121,rectum,carcinoma,0,1	POM121	131	1	1	Substitution - Missense(1)	large_intestine(1)	c.C2096T						scavenged	.						9.0	12.0	11.0					7																	72413423		1897	3928	5825	SO:0001583	missense	9883	exon11			CATATCCGGGAGC	AB014518	CCDS5542.1, CCDS59059.1	7q11.23	2013-01-08	2012-03-13		ENSG00000196313	ENSG00000196313		"""-"""	19702	protein-coding gene	gene with protein product		615753	"""POM121 membrane glycoprotein (rat)"", ""POM121 membrane glycoprotein"""			8335683, 9734811, 17900573	Standard	NM_172020		Approved	KIAA0618, DKFZP586G1822, DKFZP586P2220, POM121A	uc003twk.2	Q96HA1	OTTHUMG00000023527	ENST00000434423.2:c.2891C>T	7.37:g.72413423C>T	ENSP00000405562:p.Pro964Leu	Somatic	282	0	0		WXS	Illumina HiSeq	Phase_I	266	4	0.0150376	NM_172020	A6NFS9|A8CDT4|A8K933|A8MXF9|O75115|Q96DI0|Q9H9X1|Q9Y2N3|Q9Y4S7	Missense_Mutation	SNP	ENST00000434423.2	37		.	.	.	.	.	.	.	.	.	.	C	11.06	1.528404	0.27299	.	.	ENSG00000196313	ENST00000446813;ENST00000257622;ENST00000395270;ENST00000358357;ENST00000434423	T;T;T;T;T	0.06371	3.31;3.34;3.31;3.34;3.52	2.33	2.33	0.28932	.	0.532332	0.14207	N	0.334357	T	0.16938	0.0407	L	0.55481	1.735	0.30006	P	0.815588	D;P	0.89917	1.0;0.839	D;B	0.91635	0.999;0.287	T	0.16778	-1.0391	9	0.28530	T	0.3	.	10.1668	0.42886	0.0:1.0:0.0:0.0	.	699;964	A8MXF9;Q96HA1	.;P121A_HUMAN	L	699;699;699;699;964	ENSP00000393020:P699L;ENSP00000257622:P699L;ENSP00000378687:P699L;ENSP00000351124:P699L;ENSP00000405562:P964L	ENSP00000257622:P699L	P	+	2	0	POM121	72051359	0.041000	0.20044	0.365000	0.25901	0.077000	0.17291	2.433000	0.44793	1.309000	0.44985	0.173000	0.16961	CCG	C|0.500;T|0.500	0.500	weak		0.647	POM121-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000347344.1		
MUC5B	727897	hgsc.bcm.edu	37	11	1267562	1267562	+	Missense_Mutation	SNP	C	C	T	rs60268710	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr11:1267562C>T	ENST00000529681.1	+	31	9510	c.9452C>T	c.(9451-9453)aCg>aTg	p.T3151M	MUC5B_ENST00000447027.1_Missense_Mutation_p.T3154M|RP11-532E4.2_ENST00000532061.2_RNA	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	3151	17 X approximate tandem repeats, Ser/Thr- rich.|7 X Cys-rich subdomain repeats.|Thr-rich.			Missing (in Ref. 6; AAB61398). {ECO:0000305}.|TGPTA -> LPHG (in Ref. 4; CAA96577). {ECO:0000305}.	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)		ACTGGCCCCACGGCCACCCCG	0.677													c|||	1706	0.340655	0.2133	0.33	5008	,	,		17737	0.6012		0.2883	False		,,,				2504	0.3057				p.T3151M		Atlas-SNP	.											MUC5AC,NS,carcinoma,-1,1	MUC5B	473	1	0			c.C9452T						scavenged	.	C	MET/THR	782,3294		71,640,1327	53.0	69.0	63.0		9452	-3.5	0.0	11	dbSNP_129	63	2471,5819		394,1683,2068	no	missense	MUC5B	NM_002458.2	81	465,2323,3395	TT,TC,CC		29.807,19.1855,26.306	possibly-damaging	3151/5763	1267562	3253,9113	2038	4145	6183	SO:0001583	missense	727897	exon31			GCCCCACGGCCAC	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.9452C>T	11.37:g.1267562C>T	ENSP00000436812:p.Thr3151Met	Somatic	217	2	0.00921659		WXS	Illumina HiSeq	Phase_I	230	11	0.0478261	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	37	CCDS44515.2	769	0.35210622710622713	111	0.22560975609756098	107	0.2955801104972376	346	0.6048951048951049	205	0.2704485488126649	c	2.006	-0.428266	0.04701	0.191855	0.29807	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637;ENST00000406844	T;T	0.20332	2.08;2.26	1.73	-3.46	0.04767	.	.	.	.	.	T	0.00012	0.0000	L	0.50333	1.59	0.80722	P	0.0	P;P	0.44260	0.707;0.83	B;B	0.28139	0.029;0.086	T	0.35699	-0.9778	8	0.87932	D	0	.	5.8817	0.18858	0.0:0.1548:0.426:0.4192	rs60268710	3734;3154	A7Y9J9;E9PBJ0	.;.	M	3151;3154;3123;3111	ENSP00000436812:T3151M;ENSP00000415793:T3154M	ENSP00000343037:T3123M	T	+	2	0	MUC5B	1224138	0.000000	0.05858	0.000000	0.03702	0.017000	0.09413	-1.828000	0.01702	-1.881000	0.01123	-0.708000	0.03648	ACG	C|0.929;T|0.071	0.071	strong		0.677	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
OR7G3	390883	hgsc.bcm.edu	37	19	9237435	9237435	+	Silent	SNP	A	A	G	rs386806663|rs10407484	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr19:9237435A>G	ENST00000305444.2	-	1	191	c.192T>C	c.(190-192)tcT>tcC	p.S64S		NM_001001958.1	NP_001001958.1	Q8NG95	OR7G3_HUMAN	olfactory receptor, family 7, subfamily G, member 3	64						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.S64S(1)		NS(2)|endometrium(1)|large_intestine(3)|liver(1)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	15						AGGACAGGATAGAGAGGAGGA	0.552													G|||	2249	0.449081	0.8041	0.2421	5008	,	,		20656	0.3651		0.3141	False		,,,				2504	0.3415				p.S64S		Atlas-SNP	.											OR7G3,NS,carcinoma,0,1	OR7G3	41	1	1	Substitution - coding silent(1)	prostate(1)	c.T192C						scavenged	.	G		3080,1326		1167,746,290	128.0	102.0	110.0		192	-2.5	0.0	19	dbSNP_119	110	2659,5941		386,1887,2027	no	coding-synonymous	OR7G3	NM_001001958.1		1553,2633,2317	GG,GA,AA		30.9186,30.0953,44.1258		64/313	9237435	5739,7267	2203	4300	6503	SO:0001819	synonymous_variant	390883	exon1			CAGGATAGAGAGG		CCDS32899.1	19p13.2	2013-09-24			ENSG00000170920	ENSG00000170920		"""GPCR / Class A : Olfactory receptors"""	8467	protein-coding gene	gene with protein product							Standard	NM_001001958		Approved	OST085	uc010xkl.2	Q8NG95	OTTHUMG00000165520	ENST00000305444.2:c.192T>C	19.37:g.9237435A>G		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	115	4	0.0347826	NM_001001958	Q6IFJ6|Q96R99	Silent	SNP	ENST00000305444.2	37	CCDS32899.1																																																																																			A|0.566;G|0.434	0.434	strong		0.552	OR7G3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384611.1		
FAM126A	84668	hgsc.bcm.edu	37	7	23015831	23015831	+	Silent	SNP	T	T	C	rs3735231	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr7:23015831T>C	ENST00000432176.2	-	7	856	c.624A>G	c.(622-624)tcA>tcG	p.S208S	FAM126A_ENST00000409923.1_Silent_p.S208S	NM_032581.3	NP_115970.2	Q9BYI3	HYCCI_HUMAN	family with sequence similarity 126, member A	208					signal transduction (GO:0007165)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	signal transducer activity (GO:0004871)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(8)|urinary_tract(2)	23						TACTTTACCTTGAACAAATTT	0.318													T|||	1877	0.3748	0.3578	0.33	5008	,	,		18391	0.4663		0.3628	False		,,,				2504	0.3476				p.S208S		Atlas-SNP	.											FAM126A,NS,carcinoma,-1,1	FAM126A	53	1	0			c.A624G						scavenged	.	T		1514,2892	479.2+/-358.4	276,962,965	86.0	84.0	85.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	624	5.5	1.0	7	dbSNP_107	85	2966,5632	460.2+/-365.1	518,1930,1851	no	coding-synonymous	FAM126A	NM_032581.3		794,2892,2816	CC,CT,TT		34.4964,34.3622,34.4509		208/522	23015831	4480,8524	2203	4299	6502	SO:0001819	synonymous_variant	84668	exon7			TTACCTTGAACAA	BC018710	CCDS5377.1	7p15.3	2008-10-02			ENSG00000122591	ENSG00000122591			24587	protein-coding gene	gene with protein product	"""down regulated by Ctnnb1, a"""	610531				10910037, 16951682	Standard	NM_032581		Approved	DRCTNNB1A, HCC, HYCC1, hyccin	uc003svm.4	Q9BYI3	OTTHUMG00000128435	ENST00000432176.2:c.624A>G	7.37:g.23015831T>C		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	84	3	0.0357143	NM_032581	A4D145|Q6N010|Q75MR4|Q7LDZ4|Q96MX1|Q96NQ6	Silent	SNP	ENST00000432176.2	37	CCDS5377.1	823	0.3768315018315018	154	0.3130081300813008	130	0.35911602209944754	269	0.47027972027972026	270	0.3562005277044855	T	12.31	1.900832	0.33535	0.343622	0.344964	ENSG00000122591	ENST00000440481	.	.	.	5.49	5.49	0.81192	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.43653	-0.9378	3	.	.	.	-16.156	15.587	0.76491	0.0:0.0:0.0:1.0	rs3735231;rs10368120;rs17147509;rs58350469;rs3735231	.	.	.	R	260	.	.	Q	-	2	0	FAM126A	22982356	1.000000	0.71417	1.000000	0.80357	0.705000	0.40729	1.643000	0.37217	2.092000	0.63282	0.374000	0.22700	CAA	T|0.643;C|0.357	0.357	strong		0.318	FAM126A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250230.1	NM_032581	
ZNF839	55778	hgsc.bcm.edu	37	14	102792822	102792822	+	Silent	SNP	T	T	C			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr14:102792822T>C	ENST00000558850.1	+	2	791	c.441T>C	c.(439-441)gaT>gaC	p.D147D	ZNF839_ENST00000262236.5_Silent_p.D147D|ZNF839_ENST00000559185.1_Silent_p.D147D|ZNF839_ENST00000442396.2_Silent_p.D263D	NM_001267827.1	NP_001254756.1	A8K0R7	ZN839_HUMAN	zinc finger protein 839	147							metal ion binding (GO:0046872)			breast(2)|central_nervous_system(1)|endometrium(5)|large_intestine(2)|lung(5)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	19						AAGCTAAAGATTATAAGTTCA	0.388																																					p.D263D		Atlas-SNP	.											ZNF839,NS,carcinoma,+2,1	ZNF839	41	1	0			c.T789C						scavenged	.						41.0	41.0	41.0					14																	102792822		1846	4100	5946	SO:0001819	synonymous_variant	55778	exon2			TAAAGATTATAAG	AK093342	CCDS45164.1, CCDS58336.1	14q32.32	2010-05-06	2008-06-23	2008-06-23	ENSG00000022976	ENSG00000022976			20345	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 131"""	C14orf131			Standard	NM_018335		Approved		uc010awk.2	A8K0R7		ENST00000558850.1:c.441T>C	14.37:g.102792822T>C		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	84	2	0.0238095	NM_018335	B3KSD2|Q53FH5|Q6GPI5|Q86TU1|Q9BQ86|Q9NUU3	Silent	SNP	ENST00000558850.1	37	CCDS58336.1																																																																																			.	.	none		0.388	ZNF839-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000415492.2	NM_018335	
SPACA7	122258	hgsc.bcm.edu	37	13	113053470	113053470	+	Missense_Mutation	SNP	T	T	A	rs10816	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr13:113053470T>A	ENST00000283550.3	+	4	399	c.332T>A	c.(331-333)gTc>gAc	p.V111D	SPACA7_ENST00000375699.3_Missense_Mutation_p.V80D	NM_145248.4	NP_660291.2	Q96KW9	SPAC7_HUMAN	sperm acrosome associated 7	111			V -> D (in dbSNP:rs10816). {ECO:0000269|PubMed:15489334}.			acrosomal vesicle (GO:0001669)|extracellular region (GO:0005576)				large_intestine(5)|lung(4)|skin(3)|urinary_tract(1)	13						GGCATTGAGGTCAAAATTTCC	0.423													A|||	3340	0.666933	0.7905	0.6081	5008	,	,		18900	0.624		0.5716	False		,,,				2504	0.684				p.V111D		Atlas-SNP	.											SPACA7,NS,adenoma,0,1	SPACA7	36	1	0			c.T332A						scavenged	.	A	ASP/VAL	3445,961	360.9+/-315.4	1357,731,115	70.0	71.0	71.0		332	0.4	0.0	13	dbSNP_52	71	5185,3415	503.2+/-375.9	1577,2031,692	yes	missense	SPACA7	NM_145248.4	152	2934,2762,807	AA,AT,TT		39.7093,21.8112,33.646	benign	111/196	113053470	8630,4376	2203	4300	6503	SO:0001583	missense	122258	exon4			TTGAGGTCAAAAT	BC016750	CCDS9524.1	13q34	2013-10-11	2011-03-15	2011-03-15	ENSG00000153498	ENSG00000153498			29575	protein-coding gene	gene with protein product			"""chromosome 13 open reading frame 28"""	C13orf28		22495889	Standard	NM_145248		Approved		uc001vsd.2	Q96KW9	OTTHUMG00000017365	ENST00000283550.3:c.332T>A	13.37:g.113053470T>A	ENSP00000283550:p.Val111Asp	Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	152	5	0.0328947	NM_145248	Q5T8L1	Missense_Mutation	SNP	ENST00000283550.3	37	CCDS9524.1	1381	0.6323260073260073	382	0.7764227642276422	229	0.6325966850828729	344	0.6013986013986014	426	0.5620052770448549	A	0.743	-0.775762	0.02951	0.781888	0.602907	ENSG00000153498	ENST00000283550;ENST00000414180;ENST00000443541;ENST00000375699	T;T;T;T	0.39787	1.06;1.06;1.06;1.06	3.03	0.446	0.16602	.	.	.	.	.	T	0.00012	0.0000	N	0.04508	-0.205	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.36383	-0.9750	8	0.09843	T	0.71	-4.0574	0.5289	0.00625	0.4371:0.2203:0.129:0.2136	rs10816;rs1132162;rs3192694;rs11554437;rs17294556;rs17845503;rs17858390;rs60368660;rs10816	111	Q96KW9	SPAC7_HUMAN	D	111;99;97;80	ENSP00000283550:V111D;ENSP00000416096:V99D;ENSP00000406733:V97D;ENSP00000364851:V80D	ENSP00000283550:V111D	V	+	2	0	SPACA7	112101471	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.204000	0.09425	-0.169000	0.10834	-0.265000	0.10407	GTC	T|0.343;A|0.657	0.657	strong		0.423	SPACA7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045820.2	NM_145248	
TAS2R20	259295	hgsc.bcm.edu	37	12	11149769	11149769	+	Missense_Mutation	SNP	T	T	C	rs10845281	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr12:11149769T>C	ENST00000538986.1	-	1	705	c.706A>G	c.(706-708)Ata>Gta	p.I236V	PRR4_ENST00000536668.1_Intron|TAS2R14_ENST00000381852.4_Intron	NM_176889.2	NP_795370.2	P59543	T2R20_HUMAN	taste receptor, type 2, member 20	236			I -> V (in dbSNP:rs10845281). {ECO:0000269|PubMed:15496549}.		sensory perception of taste (GO:0050909)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(1)|endometrium(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	13						GCAAGTAATATGAGGAAGGAG	0.393													T|||	2118	0.422923	0.0651	0.3847	5008	,	,		20724	0.755		0.3817	False		,,,				2504	0.6339				p.I236V		Atlas-SNP	.											.	TAS2R20	17	.	0			c.A706G						PASS	.	T	VAL/ILE	442,3964	212.2+/-232.1	18,406,1779	154.0	152.0	152.0		706	-1.6	0.0	12	dbSNP_120	152	3016,5584	465.5+/-366.5	544,1928,1828	yes	missense	TAS2R20	NM_176889.2	29	562,2334,3607	CC,CT,TT		35.0698,10.0318,26.5877	benign	236/310	11149769	3458,9548	2203	4300	6503	SO:0001583	missense	259295	exon1			GTAATATGAGGAA	AX097732, AF494236	CCDS8639.1	12p13.2	2012-08-22			ENSG00000255837	ENSG00000255837		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	19109	protein-coding gene	gene with protein product		613962	"""taste receptor, type 2, member 49"""	TAS2R49			Standard	NM_176889		Approved	T2R20, T2R56	uc001qzm.2	P59543	OTTHUMG00000162695	ENST00000538986.1:c.706A>G	12.37:g.11149769T>C	ENSP00000441624:p.Ile236Val	Somatic	205	0	0		WXS	Illumina HiSeq	Phase_I	184	9	0.048913	NM_176889	P59549|Q2HIZ4|Q496D8|Q645X9	Missense_Mutation	SNP	ENST00000538986.1	37	CCDS8639.1	898	0.41117216117216115	33	0.06707317073170732	155	0.4281767955801105	426	0.7447552447552448	284	0.37467018469656993	T	4.775	0.144169	0.09134	0.100318	0.350698	ENSG00000255837	ENST00000538986	T	0.00864	5.6	2.66	-1.57	0.08506	.	1.555360	0.04751	U	0.424564	T	0.00012	0.0000	L	0.31476	0.935	0.80722	P	0.0	B	0.02656	0.0	B	0.09377	0.004	T	0.08166	-1.0735	9	0.62326	D	0.03	.	0.4216	0.00457	0.3201:0.1817:0.1247:0.3734	rs10845281;rs52830191;rs10845281	236	P59543	T2R20_HUMAN	V	236	ENSP00000441624:I236V	ENSP00000441624:I236V	I	-	1	0	TAS2R20	11041036	0.002000	0.14202	0.000000	0.03702	0.001000	0.01503	0.139000	0.16036	-0.493000	0.06678	-2.198000	0.00308	ATA	T|0.675;C|0.325	0.325	strong		0.393	TAS2R20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370130.2	NM_176889	
DEFB127	140850	hgsc.bcm.edu	37	20	139456	139456	+	Missense_Mutation	SNP	G	G	A	rs12624954	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr20:139456G>A	ENST00000382388.3	+	2	166	c.91G>A	c.(91-93)Gga>Aga	p.G31R		NM_139074.3	NP_620713.1	Q9H1M4	DB127_HUMAN	defensin, beta 127	31			G -> R (in dbSNP:rs12624954). {ECO:0000269|PubMed:11854508}.		defense response to bacterium (GO:0042742)|innate immune response (GO:0045087)	extracellular region (GO:0005576)				NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(4)	9		all_cancers(10;7.65e-05)|Lung NSC(37;0.0417)|all_epithelial(17;0.0676)|all_lung(30;0.0713)|Breast(17;0.231)	OV - Ovarian serous cystadenocarcinoma(29;0.122)			CTATGTACAAGGACATTGCAG	0.403													G|||	1624	0.324281	0.0424	0.3487	5008	,	,		22136	0.5446		0.3419	False		,,,				2504	0.4427				p.G31R		Atlas-SNP	.											DEFB127,NS,carcinoma,-1,1	DEFB127	15	1	0			c.G91A						PASS	.	G	ARG/GLY	395,4011	195.3+/-220.0	18,359,1826	92.0	82.0	85.0		91	3.1	0.1	20	dbSNP_120	85	3023,5577	463.2+/-365.9	518,1987,1795	yes	missense	DEFB127	NM_139074.2	125	536,2346,3621	AA,AG,GG		35.1512,8.965,26.2802	probably-damaging	31/100	139456	3418,9588	2203	4300	6503	SO:0001583	missense	140850	exon2			GTACAAGGACATT	AY358796	CCDS12991.1	20p13	2008-02-01	2002-05-09	2002-05-10	ENSG00000088782	ENSG00000088782		"""Defensins, beta"""	16206	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 73"""	C20orf73		11854508	Standard	NM_139074		Approved	bA530N10.2, DEF-27	uc002wcy.2	Q9H1M4	OTTHUMG00000031617	ENST00000382388.3:c.91G>A	20.37:g.139456G>A	ENSP00000371825:p.Gly31Arg	Somatic	279	0	0		WXS	Illumina HiSeq	Phase_I	290	12	0.0413793	NM_139074	Q14DW7	Missense_Mutation	SNP	ENST00000382388.3	37	CCDS12991.1	702	0.32142857142857145	19	0.03861788617886179	135	0.3729281767955801	287	0.5017482517482518	261	0.34432717678100266	G	10.22	1.289992	0.23478	0.08965	0.351512	ENSG00000088782	ENST00000382388	T	0.62639	0.01	3.12	3.12	0.35913	.	0.000000	0.33834	N	0.004506	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	D	0.89917	1.0	D	0.97110	1.0	T	0.47849	-0.9085	8	0.56958	D	0.05	-21.6232	9.9776	0.41793	0.0:0.0:1.0:0.0	rs12624954;rs52796717;rs61481484;rs12624954	31	Q9H1M4	DB127_HUMAN	R	31	ENSP00000371825:G31R	ENSP00000371825:G31R	G	+	1	0	DEFB127	87456	0.951000	0.32395	0.140000	0.22221	0.028000	0.11728	3.236000	0.51336	2.059000	0.61396	0.305000	0.20034	GGA	G|0.719;A|0.281	0.281	strong		0.403	DEFB127-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077429.1	NM_139074	
WDR49	151790	hgsc.bcm.edu	37	3	167320010	167320010	+	Missense_Mutation	SNP	T	T	C	rs75218075	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr3:167320010T>C	ENST00000308378.3	-	3	462	c.157A>G	c.(157-159)Aaa>Gaa	p.K53E	WDR49_ENST00000453925.2_Missense_Mutation_p.K106E|WDR49_ENST00000479765.1_Missense_Mutation_p.K394E	NM_178824.3	NP_849146.1	Q8IV35	WDR49_HUMAN	WD repeat domain 49	53										breast(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(28)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	50						CCCACTGGTTTAGAGACAACA	0.378													T|||	364	0.0726837	0.087	0.0101	5008	,	,		18820	0.2034		0.005	False		,,,				2504	0.0327				p.K53E		Atlas-SNP	.											.	WDR49	188	.	0			c.A157G						PASS	.	T	GLU/LYS	279,4127	154.8+/-188.1	7,265,1931	73.0	71.0	72.0		157	5.4	1.0	3	dbSNP_131	72	17,8583	13.3+/-46.6	1,15,4284	yes	missense	WDR49	NM_178824.3	56	8,280,6215	CC,CT,TT		0.1977,6.3323,2.2759	probably-damaging	53/698	167320010	296,12710	2203	4300	6503	SO:0001583	missense	151790	exon3			CTGGTTTAGAGAC	AK097556	CCDS3201.1	3q26.1	2013-01-11			ENSG00000174776	ENSG00000174776		"""WD repeat domain containing"""	26587	protein-coding gene	gene with protein product						12477932	Standard	NM_178824		Approved	FLJ33620	uc003fev.1	Q8IV35	OTTHUMG00000158290	ENST00000308378.3:c.157A>G	3.37:g.167320010T>C	ENSP00000311343:p.Lys53Glu	Somatic	281	0	0		WXS	Illumina HiSeq	Phase_I	257	11	0.0428016	NM_178824	Q8N297	Missense_Mutation	SNP	ENST00000308378.3	37	CCDS3201.1	152	0.0695970695970696	39	0.07926829268292683	2	0.0055248618784530384	107	0.18706293706293706	4	0.005277044854881266	T	21.9	4.219294	0.79464	0.063323	0.001977	ENSG00000174776	ENST00000308378;ENST00000479765;ENST00000453925	T;T;T	0.59906	0.23;0.23;0.23	5.4	5.4	0.78164	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.232834	0.41396	D	0.000884	T	0.00210	0.0006	L	0.52823	1.66	0.34878	D	0.744317	D;D;D	0.69078	0.957;0.957;0.997	P;P;P	0.62649	0.71;0.621;0.905	T	0.10337	-1.0634	10	0.39692	T	0.17	.	14.4309	0.67249	0.0:0.0:0.0:1.0	.	106;394;53	E7EQK3;E9PDB0;Q8IV35	.;.;WDR49_HUMAN	E	53;394;106	ENSP00000311343:K53E;ENSP00000419749:K394E;ENSP00000410863:K106E	ENSP00000311343:K53E	K	-	1	0	WDR49	168802704	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	2.996000	0.49449	2.038000	0.60285	0.455000	0.32223	AAA	T|0.965;C|0.035	0.035	strong		0.378	WDR49-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000350592.3	NM_178824	
BTBD16	118663	hgsc.bcm.edu	37	10	124096035	124096035	+	Silent	SNP	T	T	C	rs3817281	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr10:124096035T>C	ENST00000260723.4	+	15	1541	c.1290T>C	c.(1288-1290)tcT>tcC	p.S430S	BTBD16_ENST00000495370.2_3'UTR|BTBD16_ENST00000368994.2_Silent_p.S431S	NM_144587.2	NP_653188.2	Q32M84	BTBDG_HUMAN	BTB (POZ) domain containing 16	430										breast(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(5)|lung(3)|skin(2)|stomach(1)|urinary_tract(1)	15		all_neural(114;0.107)|Lung NSC(174;0.175)|all_lung(145;0.222)|Breast(234;0.238)				ACCTGGAATCTCCCTCTGCGG	0.572													C|||	2300	0.459265	0.3956	0.4856	5008	,	,		17882	0.6935		0.326	False		,,,				2504	0.4223				p.S430S		Atlas-SNP	.											.	BTBD16	44	.	0			c.T1290C						PASS	.	C		1571,2835	654.3+/-399.7	293,985,925	67.0	57.0	60.0		1290	-6.6	0.0	10	dbSNP_107	60	2746,5854	670.0+/-402.7	445,1856,1999	no	coding-synonymous	BTBD16	NM_144587.2		738,2841,2924	CC,CT,TT		31.9302,35.6559,33.1924		430/507	124096035	4317,8689	2203	4300	6503	SO:0001819	synonymous_variant	118663	exon15			GGAATCTCCCTCT	AK058088	CCDS31301.1	10q26.13	2013-01-24	2006-07-04	2006-07-04	ENSG00000138152	ENSG00000138152		"""BTB/POZ domain containing"""	26340	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 87"""	C10orf87			Standard	NM_144587		Approved	FLJ25359, Em:AC061711.1	uc001lgc.1	Q32M84	OTTHUMG00000019182	ENST00000260723.4:c.1290T>C	10.37:g.124096035T>C		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	80	5	0.0625	NM_144587	A6NM63|Q4VXL1|Q96LN0	Silent	SNP	ENST00000260723.4	37	CCDS31301.1																																																																																			T|0.613;C|0.387	0.387	strong		0.572	BTBD16-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000050780.3	NM_144587	
OR8B4	283162	hgsc.bcm.edu	37	11	124293857	124293857	+	Missense_Mutation	SNP	A	A	C	rs79770470	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr11:124293857A>C	ENST00000356130.3	-	1	932	c.911T>G	c.(910-912)cTg>cGg	p.L304R		NM_001005196.1	NP_001005196.1	Q96RC9	OR8B4_HUMAN	olfactory receptor, family 8, subfamily B, member 4	304						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(7)|lung(15)|ovary(1)|skin(6)|stomach(1)|urinary_tract(1)	32		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0279)		CACTCTCTTCAGGGTTTTGCC	0.428													A|||	15	0.00299521	0.0	0.0	5008	,	,		17636	0.0149		0.0	False		,,,				2504	0.0				p.L304R		Atlas-SNP	.											OR8B4,NS,carcinoma,-1,1	OR8B4	60	1	0			c.T911G						scavenged	.						72.0	73.0	72.0					11																	124293857		2201	4299	6500	SO:0001583	missense	283162	exon1			CTCTTCAGGGTTT	AB065831	CCDS31710.1	11q24	2012-08-09		2001-06-29	ENSG00000198657	ENSG00000198657		"""GPCR / Class A : Olfactory receptors"""	8473	protein-coding gene	gene with protein product				OR8B4P			Standard	NM_001005196		Approved		uc010sak.2	Q96RC9	OTTHUMG00000165916	ENST00000356130.3:c.911T>G	11.37:g.124293857A>C	ENSP00000348449:p.Leu304Arg	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	172	4	0.0232558	NM_001005196	B2RNF8|Q6IFQ7	Missense_Mutation	SNP	ENST00000356130.3	37	CCDS31710.1	10	0.004578754578754579	0	0.0	0	0.0	10	0.017482517482517484	0	0.0	a	19.64	3.865772	0.71949	.	.	ENSG00000198657	ENST00000356130	T	0.50548	0.74	4.19	4.19	0.49359	.	0.202836	0.24256	N	0.040122	T	0.51381	0.1671	M	0.80982	2.52	0.09310	N	1	D	0.56746	0.977	P	0.62649	0.905	T	0.56038	-0.8045	10	0.72032	D	0.01	.	13.9593	0.64168	1.0:0.0:0.0:0.0	.	304	Q96RC9	OR8B4_HUMAN	R	304	ENSP00000348449:L304R	ENSP00000348449:L304R	L	-	2	0	OR8B4	123799067	0.049000	0.20398	0.181000	0.23098	0.865000	0.49528	3.431000	0.52814	2.119000	0.64992	0.533000	0.62120	CTG	A|0.995;C|0.005	0.005	strong		0.428	OR8B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387055.1	NM_001005196	
ECD	11319	hgsc.bcm.edu	37	10	74897816	74897816	+	Silent	SNP	C	C	T	rs2271905	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr10:74897816C>T	ENST00000372979.4	-	12	1640	c.1434G>A	c.(1432-1434)gaG>gaA	p.E478E	ECD_ENST00000454759.2_Silent_p.E435E|ECD_ENST00000430082.2_Silent_p.E511E	NM_007265.2	NP_009196.1	O95905	SGT1_HUMAN	ecdysoneless homolog (Drosophila)	478					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)	p.E478E(1)		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)					TGATTGGAGCCTCAGAAGGTT	0.308													T|||	1180	0.235623	0.3676	0.1239	5008	,	,		17095	0.3145		0.0596	False		,,,				2504	0.2362				p.E511E		Atlas-SNP	.											ECD,NS,carcinoma,0,1	ECD	50	1	1	Substitution - coding silent(1)	stomach(1)	c.G1533A						scavenged	.	T	,,	1422,2984	667.3+/-401.8	226,970,1007	53.0	52.0	52.0		1533,1305,1434	-0.3	0.9	10	dbSNP_100	52	613,7987	784.4+/-407.6	30,553,3717	no	coding-synonymous,coding-synonymous,coding-synonymous	ECD	NM_001135752.1,NM_001135753.1,NM_007265.2	,,	256,1523,4724	TT,TC,CC		7.1279,32.2742,15.6466	,,	511/678,435/602,478/645	74897816	2035,10971	2203	4300	6503	SO:0001819	synonymous_variant	11319	exon13			TGGAGCCTCAGAA	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.1434G>A	10.37:g.74897816C>T		Somatic	232	0	0		WXS	Illumina HiSeq	Phase_I	251	10	0.0398406	NM_001135752	C9JX46|E9PAW8	Silent	SNP	ENST00000372979.4	37	CCDS7321.1																																																																																			C|0.809;T|0.191	0.191	strong		0.308	ECD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048606.1	NM_007265	
CACNG4	27092	hgsc.bcm.edu	37	17	65026886	65026886	+	Silent	SNP	C	C	T	rs11649752	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr17:65026886C>T	ENST00000262138.3	+	4	752	c.750C>T	c.(748-750)acC>acT	p.T250T	RP11-74H8.1_ENST00000579138.1_RNA|AC005544.1_ENST00000375684.1_5'Flank	NM_014405.3	NP_055220.1	Q9UBN1	CCG4_HUMAN	calcium channel, voltage-dependent, gamma subunit 4	250					membrane depolarization (GO:0051899)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|synaptic transmission (GO:0007268)|transmission of nerve impulse (GO:0019226)|transport (GO:0006810)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|endocytic vesicle membrane (GO:0030666)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|prostate(3)	19	all_cancers(12;9.86e-11)		BRCA - Breast invasive adenocarcinoma(6;1.35e-07)			CAAGGTCCACCGAGGCCTCGC	0.637													C|||	299	0.0597045	0.0045	0.134	5008	,	,		16727	0.0655		0.0795	False		,,,				2504	0.0552				p.T250T		Atlas-SNP	.											.	CACNG4	44	.	0			c.C750T						PASS	.	C		107,4299	82.4+/-120.9	0,107,2096	59.0	60.0	60.0		750	-10.0	0.9	17	dbSNP_120	60	905,7695	200.7+/-244.4	51,803,3446	no	coding-synonymous	CACNG4	NM_014405.3		51,910,5542	TT,TC,CC		10.5233,2.4285,7.781		250/328	65026886	1012,11994	2203	4300	6503	SO:0001819	synonymous_variant	27092	exon4			GTCCACCGAGGCC	AH008289	CCDS11667.1	17q24	2006-01-23				ENSG00000075461		"""Calcium channel subunits"""	1408	protein-coding gene	gene with protein product		606404				10613843	Standard	NM_014405		Approved	MGC11138, MGC24983	uc002jft.2	Q9UBN1		ENST00000262138.3:c.750C>T	17.37:g.65026886C>T		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	93	4	0.0430108	NM_014405	B2RCK0	Silent	SNP	ENST00000262138.3	37	CCDS11667.1																																																																																			C|0.921;T|0.079	0.079	strong		0.637	CACNG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447036.1	NM_014405	
ADD1	118	hgsc.bcm.edu	37	4	2916762	2916762	+	Missense_Mutation	SNP	C	C	G	rs4963	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr4:2916762C>G	ENST00000398129.1	+	12	1777	c.1757C>G	c.(1756-1758)tCt>tGt	p.S586C	ADD1_ENST00000264758.7_Missense_Mutation_p.S617C|ADD1_ENST00000398123.2_Missense_Mutation_p.S617C|ADD1_ENST00000513328.2_Missense_Mutation_p.S586C|ADD1_ENST00000355842.3_Missense_Mutation_p.S617C|ADD1_ENST00000503455.2_Missense_Mutation_p.S617C|ADD1_ENST00000446856.1_Missense_Mutation_p.S586C|ADD1_ENST00000398125.1_Missense_Mutation_p.S617C			P35611	ADDA_HUMAN	adducin 1 (alpha)	586			S -> C (in dbSNP:rs4963). {ECO:0000269|PubMed:10391210, ECO:0000269|PubMed:1840603}.		actin cytoskeleton organization (GO:0030036)|actin filament bundle assembly (GO:0051017)|activation of signaling protein activity involved in unfolded protein response (GO:0006987)|apoptotic process (GO:0006915)|barbed-end actin filament capping (GO:0051016)|cell morphogenesis (GO:0000902)|cell volume homeostasis (GO:0006884)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular protein metabolic process (GO:0044267)|cellular response to retinoic acid (GO:0071300)|endoplasmic reticulum unfolded protein response (GO:0030968)|erythrocyte differentiation (GO:0030218)|hemoglobin metabolic process (GO:0020027)|homeostasis of number of cells within a tissue (GO:0048873)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endocytosis (GO:0045807)|positive regulation of protein binding (GO:0032092)	cytosol (GO:0005829)|dendritic spine (GO:0043197)|F-actin capping protein complex (GO:0008290)|focal adhesion (GO:0005925)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|poly(A) RNA binding (GO:0044822)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|spectrin binding (GO:0030507)|structural molecule activity (GO:0005198)|transcription factor binding (GO:0008134)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(8)|ovary(1)|prostate(2)	22				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		CAGAAGGGCTCTGAAGGTGAG	0.597													C|||	1191	0.237819	0.1702	0.1772	5008	,	,		18849	0.4524		0.1909	False		,,,				2504	0.1994				p.S617C	Esophageal Squamous(71;505 1201 20414 34538 37449)	Atlas-SNP	.											.	ADD1	56	.	0			c.C1850G						PASS	.	C	CYS/SER,CYS/SER,CYS/SER,CYS/SER	777,3629	310.2+/-291.5	61,655,1487	98.0	96.0	96.0		1757,1850,1757,1850	4.6	0.5	4	dbSNP_52	96	1582,7018	291.6+/-300.4	143,1296,2861	yes	missense,missense,missense,missense	ADD1	NM_001119.4,NM_014189.3,NM_014190.3,NM_176801.2	112,112,112,112	204,1951,4348	GG,GC,CC		18.3953,17.635,18.1378	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	586/738,617/769,586/632,617/663	2916762	2359,10647	2203	4300	6503	SO:0001583	missense	118	exon13			AGGGCTCTGAAGG	L07261	CCDS3363.1, CCDS3364.1, CCDS43205.1, CCDS75094.1	4p16.3	2009-04-22			ENSG00000087274	ENSG00000087274			243	protein-coding gene	gene with protein product		102680				1840603	Standard	NM_001119		Approved		uc003gfq.3	P35611	OTTHUMG00000122080	ENST00000398129.1:c.1757C>G	4.37:g.2916762C>G	ENSP00000381197:p.Ser586Cys	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	103	6	0.0582524	NM_176801	A2A3N8|A2A3P0|B4DI79|D3DVR3|D3DVR4|D3DVR5|Q13734|Q14729|Q16156|Q86XM2|Q9UJB6	Missense_Mutation	SNP	ENST00000398129.1	37	CCDS43205.1	592|592	0.27106227106227104|0.27106227106227104	82|82	0.16666666666666666|0.16666666666666666	68|68	0.1878453038674033|0.1878453038674033	288|288	0.5034965034965035|0.5034965034965035	154|154	0.20316622691292877|0.20316622691292877	C|C	11.65|11.65	1.700709|1.700709	0.30142|0.30142	0.17635|0.17635	0.183953|0.183953	ENSG00000087274|ENSG00000087274	ENST00000514940;ENST00000541843|ENST00000264758;ENST00000446856;ENST00000398125;ENST00000513328;ENST00000503455;ENST00000355842;ENST00000398123;ENST00000398129	.|T;T;T;T;T;T;T;T	.|0.19250	.|2.16;2.16;2.16;2.16;2.16;2.16;2.16;2.16	5.44|5.44	4.6|4.6	0.57074|0.57074	.|.	.|0.718287	.|0.13902	.|N	.|0.354858	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.34521|0.34521	1.04|1.04	0.80722|0.80722	P|P	0.0|0.0	.|B;B;P;B;B	.|0.50943	.|0.375;0.438;0.94;0.415;0.396	.|B;B;P;B;B	.|0.52267	.|0.345;0.401;0.694;0.163;0.195	T|T	0.50021|0.50021	-0.8876|-0.8876	4|9	.|0.42905	.|T	.|0.14	-1.6519|-1.6519	16.4208|16.4208	0.83758|0.83758	0.0:0.8683:0.1317:0.0|0.0:0.8683:0.1317:0.0	rs4963;rs52811169;rs58002748;rs4963|rs4963;rs52811169;rs58002748;rs4963	.|617;586;617;586;617	.|Q86XM2;P35611;P35611-3;P35611-2;A2A3N8	.|.;ADDA_HUMAN;.;.;.	V|C	323;32|617;586;617;586;617;617;617;586	.|ENSP00000264758:S617C;ENSP00000399828:S586C;ENSP00000381193:S617C;ENSP00000421907:S586C;ENSP00000423024:S617C;ENSP00000348100:S617C;ENSP00000381191:S617C;ENSP00000381197:S586C	.|ENSP00000264758:S617C	L|S	+|+	1|2	2|0	ADD1|ADD1	2886560|2886560	0.007000|0.007000	0.16637|0.16637	0.533000|0.533000	0.28001|0.28001	0.724000|0.724000	0.41520|0.41520	1.284000|1.284000	0.33249|0.33249	1.306000|1.306000	0.44926|0.44926	-0.217000|-0.217000	0.12591|0.12591	CTG|TCT	C|0.773;G|0.227;N|0.000	0.227	strong		0.597	ADD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242840.1	NM_014189	
C3orf35	339883	hgsc.bcm.edu	37	3	37476379	37476379	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr3:37476379C>T	ENST00000328376.5	+	6	1250	c.271C>T	c.(271-273)Cca>Tca	p.P91S	C3orf35_ENST00000481400.1_3'UTR	NM_178339.2	NP_848029.2	Q8IVJ8	APRG1_HUMAN	chromosome 3 open reading frame 35	91						integral component of membrane (GO:0016021)				NS(1)|central_nervous_system(1)|endometrium(3)|large_intestine(1)|lung(2)|ovary(1)|pancreas(1)|urinary_tract(1)	11						tgactcaatcccagctgctgg	0.458																																					p.P91S		Atlas-SNP	.											.	C3orf35	21	.	0			c.C271T						PASS	.						34.0	33.0	34.0					3																	37476379		1889	4110	5999	SO:0001583	missense	339883	exon6			TCAATCCCAGCTG	AJ493599	CCDS43065.1, CCDS46792.1	3p22.3	2014-05-22			ENSG00000198590	ENSG00000198590			24082	protein-coding gene	gene with protein product	"""AP20 region protein"", ""APRG1 tumor suppressor candidate"""	611429				12543795	Standard	NM_178342		Approved	APRG1	uc003cha.4	Q8IVJ8	OTTHUMG00000155923	ENST00000328376.5:c.271C>T	3.37:g.37476379C>T	ENSP00000331625:p.Pro91Ser	Somatic	265	0	0		WXS	Illumina HiSeq	Phase_I	248	88	0.354839	NM_178339	B7ZMA0|Q8IVJ5|Q8IVJ9	Missense_Mutation	SNP	ENST00000328376.5	37	CCDS43065.1	.	.	.	.	.	.	.	.	.	.	c	4.256	0.046572	0.08243	.	.	ENSG00000198590	ENST00000328376	T	0.56611	0.45	0.565	-1.13	0.09775	.	.	.	.	.	T	0.26412	0.0645	N	0.08118	0	0.09310	N	1	B	0.15141	0.012	B	0.06405	0.002	T	0.12967	-1.0527	8	0.87932	D	0	.	.	.	.	.	91	Q8IVJ8	APRG1_HUMAN	S	91	ENSP00000331625:P91S	ENSP00000331625:P91S	P	+	1	0	C3orf35	37451383	0.027000	0.19231	0.004000	0.12327	0.004000	0.04260	-0.642000	0.05427	-0.979000	0.03529	-0.970000	0.02610	CCA	.	.	none		0.458	C3orf35-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000342344.2	NM_178338	
MUC4	4585	hgsc.bcm.edu	37	3	195511959	195511959	+	Silent	SNP	G	G	A	rs369770584		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr3:195511959G>A	ENST00000463781.3	-	2	6951	c.6492C>T	c.(6490-6492)acC>acT	p.T2164T	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Silent_p.T2164T	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)		AGGAAGTGTCGGTGACAGGAA	0.577																																					p.T2164T		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,3	MUC4	1505	3	0			c.C6492T						scavenged	.						15.0	15.0	15.0					3																	195511959		676	1556	2232	SO:0001819	synonymous_variant	4585	exon2			AGTGTCGGTGACA	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.6492C>T	3.37:g.195511959G>A		Somatic	65	1	0.0153846		WXS	Illumina HiSeq	Phase_I	57	3	0.0526316	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																																																																																			.	.	weak		0.577	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
FRG1	2483	hgsc.bcm.edu	37	4	190878551	190878551	+	Splice_Site	SNP	A	A	G			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr4:190878551A>G	ENST00000226798.4	+	6	654		c.e6-1		FRG1_ENST00000514482.1_Splice_Site	NM_004477.2	NP_004468.1	Q14331	FRG1_HUMAN	FSHD region gene 1						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)	p.?(1)		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)		TGTTTCACTTAGGGGAAAATG	0.358																																					.		Atlas-SNP	.											FRG1,NS,malignant_melanoma,0,1	FRG1	76	1	1	Unknown(1)	NS(1)	c.433-2A>G						scavenged	.						10.0	16.0	14.0					4																	190878551		2077	4234	6311	SO:0001630	splice_region_variant	2483	exon6			TCACTTAGGGGAA	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.433-1A>G	4.37:g.190878551A>G		Somatic	237	2	0.00843882		WXS	Illumina HiSeq	Phase_I	211	4	0.0189573	NM_004477	A8K775	Splice_Site	SNP	ENST00000226798.4	37	CCDS34121.1	.	.	.	.	.	.	.	.	.	.	N	13.17	2.156273	0.38021	.	.	ENSG00000109536	ENST00000226798;ENST00000524583;ENST00000531991	.	.	.	3.8	3.8	0.43715	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.8823	0.46946	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	FRG1	191115545	1.000000	0.71417	1.000000	0.80357	0.407000	0.30961	9.035000	0.93752	1.517000	0.48917	0.373000	0.22412	.	.	.	none		0.358	FRG1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000359622.4	NM_004477	Intron
GPRIN2	9721	hgsc.bcm.edu	37	10	46999601	46999601	+	Missense_Mutation	SNP	G	G	A	rs9422022	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr10:46999601G>A	ENST00000374317.1	+	3	994	c.721G>A	c.(721-723)Gtg>Atg	p.V241M	GPRIN2_ENST00000374314.4_Missense_Mutation_p.V241M	NM_014696.3	NP_055511.2	O60269	GRIN2_HUMAN	G protein regulated inducer of neurite outgrowth 2	241			V -> M (in dbSNP:rs9422022).	VR -> MREVG (in Ref. 1; BAA25440 and 3; AAH11672). {ECO:0000305}.						breast(2)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(1)|lung(6)|prostate(1)	18						CATGAGGGAGGTGAGGGCTGG	0.632													G|||	32	0.00638978	0.0023	0.0014	5008	,	,		31210	0.0139		0.0109	False		,,,				2504	0.0031				p.V241M		Atlas-SNP	.											GPRIN2,caecum,adenoma,0,1	GPRIN2	94	1	0			c.G721A						PASS	.						51.0	53.0	53.0					10																	46999601		2203	4299	6502	SO:0001583	missense	9721	exon3			AGGGAGGTGAGGG	BC011672	CCDS73101.1	10q11.22	2006-08-24	2006-08-24	2006-08-24	ENSG00000204175	ENSG00000204175			23730	protein-coding gene	gene with protein product		611240	"""KIAA0514"""	KIAA0514		9628581	Standard	NM_014696		Approved	MGC15171	uc001jec.3	O60269	OTTHUMG00000018107	ENST00000374317.1:c.721G>A	10.37:g.46999601G>A	ENSP00000363436:p.Val241Met	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	60	8	0.133333	NM_014696	Q5SVF0	Missense_Mutation	SNP	ENST00000374317.1	37	CCDS31192.1	786	0.3598901098901099	179	0.3638211382113821	126	0.34806629834254144	219	0.38286713286713286	262	0.34564643799472294	G	3.183	-0.167470	0.06461	.	.	ENSG00000204175	ENST00000374317;ENST00000374314	T;T	0.03496	3.91;3.91	5.12	-1.64	0.08318	.	1.524420	0.04254	N	0.339078	T	0.00012	0.0000	L	0.34521	1.04	0.09310	N	1	B	0.15473	0.013	B	0.09377	0.004	T	0.46978	-0.9152	10	0.27082	T	0.32	0.3266	1.758	0.02986	0.326:0.1295:0.4122:0.1323	rs9422022	241	O60269	GRIN2_HUMAN	M	241	ENSP00000363436:V241M;ENSP00000363433:V241M	ENSP00000363433:V241M	V	+	1	0	GPRIN2	46419607	0.099000	0.21834	0.004000	0.12327	0.003000	0.03518	0.140000	0.16056	-0.217000	0.10033	-0.498000	0.04607	GTG	G|0.638;A|0.362	0.362	strong		0.632	GPRIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047836.1	NM_014696	
CENPC	1060	hgsc.bcm.edu	37	4	68380215	68380215	+	Missense_Mutation	SNP	G	G	A	rs11250	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr4:68380215G>A	ENST00000273853.6	-	8	1271	c.1021C>T	c.(1021-1023)Ctt>Ttt	p.L341F		NM_001812.2	NP_001803.2	Q03188	CENPC_HUMAN	centromere protein C	341			L -> F (in dbSNP:rs11250). {ECO:0000269|PubMed:1339310, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:18669648, ECO:0000269|Ref.3}.		chromosome segregation (GO:0007059)|kinetochore assembly (GO:0051382)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	condensed nuclear chromosome, centromeric region (GO:0000780)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|nucleus (GO:0005634)|pericentric heterochromatin (GO:0005721)	centromeric DNA binding (GO:0019237)|DNA binding (GO:0003677)										CTACCTTGAAGGAGTGCAGTG	0.423													G|||	3509	0.700679	0.6195	0.7536	5008	,	,		15463	0.8274		0.6252	False		,,,				2504	0.7198				p.L341F		Atlas-SNP	.											.	CENPC1	66	.	0			c.C1021T						PASS	.	G	PHE/LEU	2383,1395		748,887,254	91.0	84.0	86.0		1021	2.5	0.0	4	dbSNP_52	86	4963,3267		1501,1961,653	no	missense	CENPC1	NM_001812.2	22	2249,2848,907	AA,AG,GG		39.6962,36.9243,38.8241	probably-damaging	341/944	68380215	7346,4662	1889	4115	6004	SO:0001583	missense	1060	exon8			CTTGAAGGAGTGC	M95724	CCDS47063.1	4q13.2	2013-11-05	2013-07-03	2013-07-03	ENSG00000145241	ENSG00000145241			1854	protein-coding gene	gene with protein product		117141	"""centromere protein C 1"""	CENPC1		7959789	Standard	XR_245245		Approved	CENP-C, hcp-4, MIF2	uc003hdd.1	Q03188	OTTHUMG00000160735	ENST00000273853.6:c.1021C>T	4.37:g.68380215G>A	ENSP00000273853:p.Leu341Phe	Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	154	8	0.0519481	NM_001812	Q8IW27|Q9P0M5	Missense_Mutation	SNP	ENST00000273853.6	37	CCDS47063.1	1502	0.6877289377289377	305	0.6199186991869918	266	0.7348066298342542	467	0.8164335664335665	464	0.6121372031662269	G	13.09	2.133139	0.37630	0.630757	0.603038	ENSG00000145241	ENST00000273853	.	.	.	4.33	2.53	0.30540	.	0.867721	0.09737	N	0.762418	T	0.00012	0.0000	L	0.32530	0.975	0.80722	P	0.0	D	0.55385	0.971	P	0.50440	0.641	T	0.41197	-0.9522	8	0.10111	T	0.7	0.442	4.5934	0.12319	0.1122:0.0:0.6679:0.2199	rs11250;rs3197405;rs17017002;rs17554462;rs17854082;rs60532044;rs11250	341	Q03188	CENPC_HUMAN	F	341	.	ENSP00000273853:L341F	L	-	1	0	CENPC1	68062810	0.006000	0.16342	0.001000	0.08648	0.014000	0.08584	0.538000	0.23160	1.121000	0.41925	0.655000	0.94253	CTT	G|0.299;A|0.701	0.701	strong		0.423	CENPC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362001.2		
GPRC6A	222545	hgsc.bcm.edu	37	6	117114223	117114223	+	Silent	SNP	T	T	A	rs6924002	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr6:117114223T>A	ENST00000310357.3	-	6	1884	c.1863A>T	c.(1861-1863)acA>acT	p.T621T	GPRC6A_ENST00000530250.1_Silent_p.T446T|GPRC6A_ENST00000368549.3_Silent_p.T550T	NM_148963.2	NP_683766.2	Q5T6X5	GPC6A_HUMAN	G protein-coupled receptor, class C, group 6, member A	621					calcium-mediated signaling (GO:0019722)|response to amino acid (GO:0043200)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			autonomic_ganglia(1)|breast(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(8)|liver(1)|lung(24)|ovary(5)|pancreas(1)|skin(5)|stomach(3)|upper_aerodigestive_tract(3)	65		all_cancers(87;0.0314)|all_epithelial(87;0.0216)|Colorectal(196;0.234)		GBM - Glioblastoma multiforme(226;0.0265)|all cancers(137;0.0554)|OV - Ovarian serous cystadenocarcinoma(136;0.07)		TCACAACAGGTGTGTTCAGGT	0.433													T|||	1607	0.320887	0.1989	0.3703	5008	,	,		19816	0.5228		0.3082	False		,,,				2504	0.2556				p.T621T		Atlas-SNP	.											.	GPRC6A	152	.	0			c.A1863T						PASS	.	T		917,3489	352.1+/-311.5	94,729,1380	100.0	97.0	98.0		1863	-2.1	1.0	6	dbSNP_116	98	2837,5763	447.3+/-361.5	458,1921,1921	no	coding-synonymous	GPRC6A	NM_148963.2		552,2650,3301	AA,AT,TT		32.9884,20.8125,28.8636		621/927	117114223	3754,9252	2203	4300	6503	SO:0001819	synonymous_variant	222545	exon6			AACAGGTGTGTTC	AF502962	CCDS5112.1, CCDS69184.1, CCDS69185.1	6q22.31	2014-01-30	2014-01-30		ENSG00000173612	ENSG00000173612		"""GPCR / Class C : Calcium-sensing receptors"""	18510	protein-coding gene	gene with protein product			"""G protein-coupled receptor, family C, group 6, member A"""				Standard	NM_001286354		Approved	bA86F4.3	uc003pxj.1	Q5T6X5	OTTHUMG00000015447	ENST00000310357.3:c.1863A>T	6.37:g.117114223T>A		Somatic	224	0	0		WXS	Illumina HiSeq	Phase_I	126	11	0.0873016	NM_148963	Q6JK43|Q6JK44|Q8NGU8|Q8NHZ9|Q8TDT6	Silent	SNP	ENST00000310357.3	37	CCDS5112.1																																																																																			T|0.683;A|0.317	0.317	strong		0.433	GPRC6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041966.2		
LILRB3	11025	hgsc.bcm.edu	37	19	54721042	54721042	+	Missense_Mutation	SNP	T	T	C			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr19:54721042T>C	ENST00000391750.1	-	14	1952	c.1816A>G	c.(1816-1818)Aag>Gag	p.K606E	LILRB3_ENST00000469273.1_5'UTR|LILRA6_ENST00000419410.2_Missense_Mutation_p.K607E|LILRB3_ENST00000407860.2_Missense_Mutation_p.K623E|LILRA6_ENST00000440558.2_Missense_Mutation_p.K606E|LILRA6_ENST00000270464.5_Missense_Mutation_p.K607E|LILRA6_ENST00000391735.3_3'UTR|LILRB3_ENST00000346401.6_Missense_Mutation_p.K618E|LILRB3_ENST00000424807.1_Missense_Mutation_p.K606E|LILRB3_ENST00000245620.9_Missense_Mutation_p.K607E			O75022	LIRB3_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 3	606					cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|immune system process (GO:0002376)|negative regulation of osteoclast differentiation (GO:0045671)	integral component of plasma membrane (GO:0005887)	receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			endometrium(3)|kidney(13)|large_intestine(1)|lung(6)|ovary(2)|prostate(5)|skin(2)|stomach(1)|urinary_tract(1)	34	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)		TCAGTTGCCTTCCGTCTAAGG	0.627																																					p.K607E		Atlas-SNP	.											LILRB3,NS,carcinoma,0,1	LILRB3	67	1	0			c.A1819G						scavenged	.						108.0	108.0	108.0					19																	54721042		2202	4300	6502	SO:0001583	missense	11025	exon13			TTGCCTTCCGTCT	U91928	CCDS33105.1, CCDS46175.1	19q13.4	2013-01-11			ENSG00000204577	ENSG00000204577		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6607	protein-coding gene	gene with protein product		604820				9278324, 9382880	Standard	NM_006864		Approved	LIR-3, HL9, ILT5, LIR3, CD85a	uc002qee.1	O75022	OTTHUMG00000066626	ENST00000391750.1:c.1816A>G	19.37:g.54721042T>C	ENSP00000375630:p.Lys606Glu	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	167	5	0.0299401	NM_001081450	C9J1P3|C9JIP1|O15471|Q86U49	Missense_Mutation	SNP	ENST00000391750.1	37	CCDS33105.1	.	.	.	.	.	.	.	.	.	.	T	0.011	-1.739940	0.00675	.	.	ENSG00000204577;ENSG00000204577;ENSG00000204577;ENSG00000204577;ENSG00000204577;ENSG00000244482;ENSG00000244482;ENSG00000244482	ENST00000391750;ENST00000424807;ENST00000346401;ENST00000245620;ENST00000407860;ENST00000440558;ENST00000270464;ENST00000419410	T;T;T;T;T;T;T;T	0.00490	7.07;7.07;7.03;7.06;7.03;7.07;7.07;7.09	2.64	-4.43	0.03568	.	.	.	.	.	T	0.00109	0.0003	N	0.00746	-1.225	0.09310	N	1	B;B;B;B;B;B;B	0.16802	0.001;0.007;0.0;0.019;0.001;0.001;0.001	B;B;B;B;B;B;B	0.19391	0.003;0.007;0.001;0.025;0.006;0.003;0.005	T	0.33624	-0.9861	9	0.02654	T	1	.	4.0644	0.09854	0.0:0.3045:0.3422:0.3533	.	623;606;607;618;623;606;607	B5MCX0;F8WCY4;D3YTC4;F8W6G6;O75022-2;O75022;O75022-3	.;.;.;.;.;LIRB3_HUMAN;.	E	606;606;618;607;623;606;607;607	ENSP00000375630:K606E;ENSP00000412771:K606E;ENSP00000345184:K618E;ENSP00000245620:K607E;ENSP00000384274:K623E;ENSP00000390120:K606E;ENSP00000270464:K607E;ENSP00000411227:K607E	ENSP00000270464:K607E	K	-	1	0	LILRB3;LILRA6	59412854	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-1.125000	0.03257	-0.821000	0.04312	-1.525000	0.00928	AAG	.	.	none		0.627	LILRB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000142844.5	NM_006864	
MUC2	4583	hgsc.bcm.edu	37	11	1087972	1087972	+	Silent	SNP	C	C	T	rs10902088	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr11:1087972C>T	ENST00000441003.2	+	25	3474	c.3447C>T	c.(3445-3447)aaC>aaT	p.N1149N	MUC2_ENST00000359061.5_Silent_p.N1149N	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	1149					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)	GGACCATCAACGGCATCCACT	0.622													C|||	1641	0.327676	0.3759	0.3631	5008	,	,		15887	0.3899		0.2167	False		,,,				2504	0.2873				p.N1149N		Atlas-SNP	.											.	MUC2	614	.	0			c.C3447T						PASS	.			1440,2836		247,946,945	56.0	61.0	60.0		3447	-2.9	0.0	11	dbSNP_120	60	1693,6791		174,1345,2723	no	coding-synonymous	MUC2	NM_002457.2		421,2291,3668	TT,TC,CC		19.9552,33.6763,24.5533		1149/2813	1087972	3133,9627	2138	4242	6380	SO:0001819	synonymous_variant	4583	exon25			CATCAACGGCATC	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.3447C>T	11.37:g.1087972C>T		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	140	10	0.0714286	NM_002457	Q14878	Silent	SNP	ENST00000441003.2	37																																																																																				C|0.712;T|0.288	0.288	strong		0.622	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
SPINK5	11005	hgsc.bcm.edu	37	5	147481430	147481430	+	Silent	SNP	A	A	G	rs6896303	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr5:147481430A>G	ENST00000256084.7	+	15	1431	c.1389A>G	c.(1387-1389)ggA>ggG	p.G463G	SPINK5_ENST00000359874.3_Silent_p.G463G|SPINK5_ENST00000398454.1_Silent_p.G463G	NM_006846.3	NP_006837.2	Q9NQ38	ISK5_HUMAN	serine peptidase inhibitor, Kazal type 5	463	Kazal-like 7. {ECO:0000255|PROSITE- ProRule:PRU00798}.				anagen (GO:0042640)|epidermal cell differentiation (GO:0009913)|epithelial cell differentiation (GO:0030855)|extracellular matrix organization (GO:0030198)|hair cell differentiation (GO:0035315)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of immune response (GO:0050777)|negative regulation of proteolysis (GO:0045861)|negative regulation of serine-type peptidase activity (GO:1902572)|regulation of cell adhesion (GO:0030155)|regulation of T cell differentiation (GO:0045580)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|epidermal lamellar body (GO:0097209)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|perinuclear region of cytoplasm (GO:0048471)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.G463G(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(16)|ovary(4)|prostate(1)|skin(5)|stomach(8)|upper_aerodigestive_tract(2)	64			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCCCAGATGGAAAAATGCATG	0.502													G|||	2168	0.432907	0.1989	0.6167	5008	,	,		16733	0.4851		0.4861	False		,,,				2504	0.5102				p.G463G		Atlas-SNP	.											SPINK5,NS,carcinoma,0,1	SPINK5	245	1	1	Substitution - coding silent(1)	stomach(1)	c.A1389G						scavenged	.	G	,,	956,2828		123,710,1059	108.0	105.0	106.0		1389,1389,1389	0.3	0.7	5	dbSNP_116	106	4220,4016		1070,2080,968	no	coding-synonymous,coding-synonymous,coding-synonymous	SPINK5	NM_001127698.1,NM_001127699.1,NM_006846.3	,,	1193,2790,2027	GG,GA,AA		48.7615,25.2643,43.0616	,,	463/1095,463/917,463/1065	147481430	5176,6844	1892	4118	6010	SO:0001819	synonymous_variant	11005	exon15			AGATGGAAAAATG	AJ228139	CCDS43382.1, CCDS47300.1, CCDS47301.1	5q31-q32	2014-09-17	2005-08-17		ENSG00000133710	ENSG00000133710		"""Serine peptidase inhibitors, Kazal type"""	15464	protein-coding gene	gene with protein product	"""lymphoepithelial Kazal-type-related inhibitor"""	605010	"""serine protease inhibitor, Kazal type 5"""			10419450	Standard	NM_001127698		Approved	VAKTI, LEKTI, LETKI, NETS, NS, FLJ21544, FLJ97536, FLJ97596, FLJ99794, DKFZp686K19184	uc003loy.2	Q9NQ38	OTTHUMG00000134305	ENST00000256084.7:c.1389A>G	5.37:g.147481430A>G		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	115	4	0.0347826	NM_001127699	A8MYE8|B7WPB7|D6REN5|O75770|Q3LX95|Q3LX96|Q3LX97|Q96PP2|Q96PP3	Silent	SNP	ENST00000256084.7	37	CCDS43382.1																																																																																			A|0.545;G|0.455	0.455	strong		0.502	SPINK5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000259215.2	NM_001127698	
ZNF234	10780	hgsc.bcm.edu	37	19	44652954	44652954	+	Missense_Mutation	SNP	G	G	A	rs2293587	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr19:44652954G>A	ENST00000426739.2	+	4	304	c.46G>A	c.(46-48)Gtc>Atc	p.V16I	ZNF234_ENST00000590748.1_3'UTR|ZNF234_ENST00000592437.1_Missense_Mutation_p.V16I	NM_006630.2	NP_006621.1	Q14588	ZN234_HUMAN	zinc finger protein 234	16	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.		V -> I (in dbSNP:rs2293587).		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)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(11)|ovary(1)|prostate(1)	23		Prostate(69;0.0435)				TGTGGCTGTGGTCTTCACTGA	0.483													G|||	1614	0.322284	0.2988	0.2767	5008	,	,		18565	0.4008		0.3121	False		,,,				2504	0.316				p.V16I		Atlas-SNP	.											.	ZNF234	132	.	0			c.G46A						PASS	.	G	ILE/VAL,ILE/VAL	1228,3178	424.5+/-340.5	176,876,1151	209.0	210.0	210.0		46,46	-1.1	0.9	19	dbSNP_100	210	3029,5571	467.2+/-367.0	563,1903,1834	yes	missense,missense	ZNF234	NM_001144824.1,NM_006630.2	29,29	739,2779,2985	AA,AG,GG		35.2209,27.8711,32.731	benign,benign	16/701,16/701	44652954	4257,8749	2203	4300	6503	SO:0001583	missense	10780	exon4			GCTGTGGTCTTCA	X78927	CCDS46101.1	19q13	2013-01-08				ENSG00000263002		"""Zinc fingers, C2H2-type"", ""-"""	13027	protein-coding gene	gene with protein product		604750		ZNF269		7865130	Standard	NM_006630		Approved	HZF4	uc002oyl.4	Q14588		ENST00000426739.2:c.46G>A	19.37:g.44652954G>A	ENSP00000400878:p.Val16Ile	Somatic	223	0	0		WXS	Illumina HiSeq	Phase_I	191	8	0.0418848	NM_006630	A8K1C8|Q96IR4|Q9NS45|Q9NYT7	Missense_Mutation	SNP	ENST00000426739.2	37	CCDS46101.1	720	0.32967032967032966	146	0.2967479674796748	113	0.31215469613259667	228	0.3986013986013986	233	0.3073878627968338	G	11.40	1.628303	0.28978	0.278711	0.352209	ENSG00000167380	ENST00000426739	T	0.01725	4.67	3.85	-1.13	0.09775	Krueppel-associated box (4);	.	.	.	.	T	0.00012	0.0000	L	0.38175	1.15	0.48696	P	3.0799999999997496E-4	B	0.27625	0.183	B	0.28916	0.096	T	0.36744	-0.9735	8	0.35671	T	0.21	.	5.0799	0.14651	0.2585:0.0:0.6053:0.1362	rs2293587;rs2293587	16	Q14588	ZN234_HUMAN	I	16	ENSP00000400878:V16I	ENSP00000400878:V16I	V	+	1	0	ZNF226	49344794	0.772000	0.28567	0.895000	0.35142	0.967000	0.64934	0.782000	0.26788	-0.212000	0.10109	0.561000	0.74099	GTC	G|0.660;A|0.340	0.340	strong		0.483	ZNF234-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460586.2		
PLEKHH2	130271	hgsc.bcm.edu	37	2	43953574	43953574	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr2:43953574G>A	ENST00000282406.4	+	17	2815	c.2705G>A	c.(2704-2706)gGa>gAa	p.G902E		NM_172069.3	NP_742066.2	Q8IVE3	PKHH2_HUMAN	pleckstrin homology domain containing, family H (with MyTH4 domain) member 2	902	PH 2. {ECO:0000255|PROSITE- ProRule:PRU00145}.				negative regulation of actin filament depolymerization (GO:0030835)	cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)	actin binding (GO:0003779)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(12)|lung(24)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	56		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)				CTCCTAATTGGATCCAAGCAT	0.328																																					p.G902E		Atlas-SNP	.											.	PLEKHH2	156	.	0			c.G2705A						PASS	.						92.0	88.0	89.0					2																	43953574		2203	4300	6503	SO:0001583	missense	130271	exon17			TAATTGGATCCAA	AB095948	CCDS1812.1	2p22	2013-01-10			ENSG00000152527	ENSG00000152527		"""Pleckstrin homology (PH) domain containing"""	30506	protein-coding gene	gene with protein product		612723					Standard	NM_172069		Approved	KIAA2028, PLEKHH1L	uc010yny.2	Q8IVE3	OTTHUMG00000128657	ENST00000282406.4:c.2705G>A	2.37:g.43953574G>A	ENSP00000282406:p.Gly902Glu	Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	190	8	0.0421053	NM_172069	Q5JPJ6|Q6P4Q1|Q8N3Q3	Missense_Mutation	SNP	ENST00000282406.4	37	CCDS1812.1	.	.	.	.	.	.	.	.	.	.	G	17.46	3.394856	0.62066	.	.	ENSG00000152527	ENST00000282406	T	0.19806	2.12	5.57	5.57	0.84162	Pleckstrin homology-type (1);Pleckstrin homology domain (2);	0.114213	0.64402	D	0.000011	T	0.19525	0.0469	L	0.31664	0.95	0.52501	D	0.999952	B;P	0.35155	0.232;0.487	B;B	0.35470	0.11;0.203	T	0.02471	-1.1154	10	0.28530	T	0.3	-15.3726	19.5645	0.95388	0.0:0.0:1.0:0.0	.	902;339	Q8IVE3;Q8IVE3-2	PKHH2_HUMAN;.	E	902	ENSP00000282406:G902E	ENSP00000282406:G902E	G	+	2	0	PLEKHH2	43807078	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.928000	0.70088	2.599000	0.87857	0.650000	0.86243	GGA	.	.	none		0.328	PLEKHH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250537.1	NM_172069	
PRB4	5545	hgsc.bcm.edu	37	12	11461738	11461738	+	Missense_Mutation	SNP	G	G	C	rs79562958		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr12:11461738G>C	ENST00000535904.1	-	3	212	c.179C>G	c.(178-180)cCa>cGa	p.P60R	PRB4_ENST00000445719.2_Missense_Mutation_p.P60R|PRB4_ENST00000279575.1_Missense_Mutation_p.P60R			P10163	PRB4_HUMAN	proline-rich protein BstNI subfamily 4	81	9.5 X 21 AA tandem repeats of K-P-[EQ]- [GR]-[PR]-[PR]-P-Q-G-G-N-Q-[PS]-[QH]- [RG]-[PT]-P-P-[PH]-P-G.					extracellular region (GO:0005576)				breast(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(12)|ovary(1)|skin(4)|upper_aerodigestive_tract(3)	30						TTGTGGGGGTGGTCCTTGTGG	0.627										HNSCC(22;0.051)																											p.P60R		Atlas-SNP	.											PRB4,NS,carcinoma,0,1	PRB4	59	1	0			c.C179G						scavenged	.						209.0	226.0	220.0					12																	11461738		2201	4296	6497	SO:0001583	missense	5545	exon3			GGGGGTGGTCCTT		CCDS8641.1, CCDS58208.1	12p13.2	2012-10-02			ENSG00000230657	ENSG00000230657			9340	protein-coding gene	gene with protein product		180990					Standard	NM_002723		Approved		uc001qzt.4	P10163	OTTHUMG00000169116	ENST00000535904.1:c.179C>G	12.37:g.11461738G>C	ENSP00000442834:p.Pro60Arg	Somatic	29	2	0.0689655		WXS	Illumina HiSeq	Phase_I	47	3	0.0638298	NM_001261399	A1L439|O00600|P02813|P10161|P10162|P81489	Missense_Mutation	SNP	ENST00000535904.1	37	CCDS8641.1	.	.	.	.	.	.	.	.	.	.	.	1.271	-0.613089	0.03690	.	.	ENSG00000230657	ENST00000279575;ENST00000535904;ENST00000445719	T;T;T	0.05786	3.39;3.39;3.39	0.956	0.01	0.14081	.	.	.	.	.	T	0.03348	0.0097	N	0.25286	0.73	0.19300	N	0.999979	B	0.11235	0.004	B	0.06405	0.002	T	0.48091	-0.9065	9	0.07644	T	0.81	.	4.8976	0.13759	0.0:0.3926:0.6074:0.0	.	60	E9PAL0	.	R	60	ENSP00000279575:P60R;ENSP00000442834:P60R;ENSP00000412740:P60R	ENSP00000279575:P60R	P	-	2	0	PRB4	11353005	0.008000	0.16893	0.012000	0.15200	0.040000	0.13550	-0.216000	0.09266	-0.009000	0.14296	-1.127000	0.01993	CCA	C|1.000;|0.000	1.000	weak		0.627	PRB4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000402308.1	NM_002723	
TOX2	84969	hgsc.bcm.edu	37	20	42694462	42694462	+	Silent	SNP	G	G	A	rs148482710	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr20:42694462G>A	ENST00000358131.5	+	6	1225	c.1017G>A	c.(1015-1017)acG>acA	p.T339T	TOX2_ENST00000423191.2_Silent_p.T315T|TOX2_ENST00000435864.2_3'UTR|TOX2_ENST00000341197.4_Silent_p.T357T|TOX2_ENST00000372999.1_Silent_p.T315T	NM_001098798.1	NP_001092268.1	Q96NM4	TOX2_HUMAN	TOX high mobility group box family member 2	339					female gonad development (GO:0008585)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to gonadotropin (GO:0034698)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(13)|ovary(1)|skin(2)	26		Myeloproliferative disorder(115;0.00452)	COAD - Colon adenocarcinoma(18;0.00189)			CCTTCCTGACGCCGTCGGACC	0.662													G|||	3	0.000599042	0.0015	0.0	5008	,	,		12771	0.001		0.0	False		,,,				2504	0.0				p.T357T		Atlas-SNP	.											TOX2_ENST00000348077,right_lower_lobe,carcinoma,0,2	TOX2	158	2	0			c.G1071A						scavenged	.	G	,,,	5,4401	9.9+/-24.2	0,5,2198	78.0	83.0	81.0		945,1071,1017,945	-2.1	0.9	20	dbSNP_134	81	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TOX2	NM_001098796.1,NM_001098797.1,NM_001098798.1,NM_032883.2	,,,	0,5,6498	AA,AG,GG		0.0,0.1135,0.0384	,,,	315/465,357/507,339/489,315/465	42694462	5,13001	2203	4300	6503	SO:0001819	synonymous_variant	84969	exon7			CCTGACGCCGTCG	BC007636	CCDS13324.1, CCDS42875.1, CCDS46603.1	20q13.12	2007-03-20	2007-03-20	2007-03-20					16095	protein-coding gene	gene with protein product	"""granulosa cell HMG box 1"""	611163	"""chromosome 20 open reading frame 100"""	C20orf100		14764631	Standard	NM_001098796		Approved	dJ1108D11.2, GCX-1	uc010ggo.3	Q96NM4		ENST00000358131.5:c.1017G>A	20.37:g.42694462G>A		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	132	3	0.0227273	NM_001098797	A8K1J1|E1P5X0|G3XAC7|Q5TE33|Q5TE34|Q5TE35|Q96IC9|Q9BQN5	Silent	SNP	ENST00000358131.5	37	CCDS42875.1																																																																																			G|0.999;A|0.001	0.001	strong		0.662	TOX2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000079329.2		
AP1M2	10053	hgsc.bcm.edu	37	19	10692000	10692000	+	Silent	SNP	T	T	C	rs1045361	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr19:10692000T>C	ENST00000250244.6	-	6	697	c.615A>G	c.(613-615)tcA>tcG	p.S205S	AP1M2_ENST00000590923.1_Silent_p.S205S	NM_005498.4	NP_005489.2	Q9Y6Q5	AP1M2_HUMAN	adaptor-related protein complex 1, mu 2 subunit	205	MHD. {ECO:0000255|PROSITE- ProRule:PRU00404}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|membrane organization (GO:0061024)|post-Golgi vesicle-mediated transport (GO:0006892)|protein targeting (GO:0006605)|regulation of defense response to virus by virus (GO:0050690)|vesicle targeting (GO:0006903)|viral process (GO:0016032)	clathrin adaptor complex (GO:0030131)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|Golgi membrane (GO:0000139)|lysosomal membrane (GO:0005765)|trans-Golgi network membrane (GO:0032588)				endometrium(4)|large_intestine(1)|lung(1)|ovary(2)|urinary_tract(1)	9			Epithelial(33;1.58e-05)|all cancers(31;6.36e-05)			CTGGCATTCCTGACAGAAACA	0.557											OREG0025241	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	t|||	1866	0.372604	0.2557	0.5115	5008	,	,		19255	0.6627		0.1779	False		,,,				2504	0.3333				p.S205S		Atlas-SNP	.											AP1M2,colon,carcinoma,0,1	AP1M2	35	1	0			c.A615G						scavenged	.	T		924,3180		101,722,1229	51.0	54.0	53.0		615	-10.6	0.0	19	dbSNP_86	53	1683,6737		165,1353,2692	yes	coding-synonymous	AP1M2	NM_005498.4		266,2075,3921	CC,CT,TT		19.9881,22.5146,20.816		205/424	10692000	2607,9917	2052	4210	6262	SO:0001819	synonymous_variant	10053	exon6			CATTCCTGACAGA	AF020797	CCDS45964.1	19p13.2	2008-10-07				ENSG00000129354			558	protein-coding gene	gene with protein product		607309				10338135	Standard	NM_005498		Approved	HSMU1B, mu2, AP1-mu2	uc002mpc.3	Q9Y6Q5		ENST00000250244.6:c.615A>G	19.37:g.10692000T>C		Somatic	124	0	0	666	WXS	Illumina HiSeq	Phase_I	151	6	0.0397351	NM_005498	B2RDV5|Q9BSI8	Silent	SNP	ENST00000250244.6	37	CCDS45964.1																																																																																			T|0.749;C|0.251	0.251	strong		0.557	AP1M2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000452034.1		
COL24A1	255631	hgsc.bcm.edu	37	1	86512536	86512536	+	Missense_Mutation	SNP	C	C	T	rs60891279	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr1:86512536C>T	ENST00000370571.2	-	12	2288	c.1922G>A	c.(1921-1923)cGt>cAt	p.R641H	COL24A1_ENST00000436319.1_Missense_Mutation_p.R641H	NM_152890.5	NP_690850.2	Q17RW2	COOA1_HUMAN	collagen, type XXIV, alpha 1	641			R -> H (in dbSNP:rs60891279).		extracellular matrix organization (GO:0030198)|hematopoietic progenitor cell differentiation (GO:0002244)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)			NS(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(9)|liver(1)|lung(56)|ovary(4)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	101				all cancers(265;0.0627)|Epithelial(280;0.0689)		cttctttccacggatcccagg	0.313													C|||	921	0.183906	0.1097	0.2651	5008	,	,		17486	0.2788		0.1322	False		,,,				2504	0.182				p.R641H		Atlas-SNP	.											COL24A1,NS,carcinoma,-1,1	COL24A1	202	1	0			c.G1922A						scavenged	.	C	HIS/ARG	404,3202		20,364,1419	114.0	114.0	114.0		1922	4.2	1.0	1	dbSNP_129	114	1200,6924		77,1046,2939	yes	missense	COL24A1	NM_152890.5	29	97,1410,4358	TT,TC,CC		14.771,11.2035,13.6743	benign	641/1715	86512536	1604,10126	1803	4062	5865	SO:0001583	missense	255631	exon12			TTTCCACGGATCC	AF410793	CCDS41353.1	1p22.3-p22.2	2013-01-16			ENSG00000171502	ENSG00000171502		"""Collagens"""	20821	protein-coding gene	gene with protein product		610025					Standard	NM_152890		Approved		uc001dlj.3	Q17RW2	OTTHUMG00000010629	ENST00000370571.2:c.1922G>A	1.37:g.86512536C>T	ENSP00000359603:p.Arg641His	Somatic	446	1	0.00224215		WXS	Illumina HiSeq	Phase_I	397	10	0.0251889	NM_152890	C9J1X6|Q14BD7|Q59EX5|Q5VY50|Q7Z5L5	Missense_Mutation	SNP	ENST00000370571.2	37	CCDS41353.1	402	0.18406593406593408	59	0.11991869918699187	84	0.23204419889502761	161	0.28146853146853146	98	0.12928759894459102	C	11.28	1.591078	0.28357	0.112035	0.14771	ENSG00000171502	ENST00000370571;ENST00000436319	D;D	0.95035	-3.59;-3.59	4.22	4.22	0.49857	.	0.000000	0.38272	N	0.001752	D	0.86171	0.5869	L	0.38953	1.18	0.35679	P	0.18606299999999998	B;B	0.18013	0.025;0.004	B;B	0.13407	0.009;0.002	T	0.83293	-0.0032	9	0.41790	T	0.15	.	12.3912	0.55360	0.0:1.0:0.0:0.0	rs60891279	641;641	F8WDM8;Q17RW2	.;COOA1_HUMAN	H	641	ENSP00000359603:R641H;ENSP00000392531:R641H	ENSP00000359603:R641H	R	-	2	0	COL24A1	86285124	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.707000	0.37888	2.616000	0.88540	0.655000	0.94253	CGT	C|0.832;T|0.168	0.168	strong		0.313	COL24A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029335.4	NM_152890	
PDZRN4	29951	hgsc.bcm.edu	37	12	41946463	41946463	+	Silent	SNP	C	C	T	rs74569207	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr12:41946463C>T	ENST00000402685.2	+	6	1217	c.1209C>T	c.(1207-1209)gtC>gtT	p.V403V	PDZRN4_ENST00000298919.7_Silent_p.V143V|PDZRN4_ENST00000539469.2_Silent_p.V145V	NM_001164595.1	NP_001158067.1	Q6ZMN7	PZRN4_HUMAN	PDZ domain containing ring finger 4	403	PDZ 2. {ECO:0000255|PROSITE- ProRule:PRU00143}.						ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(23)|lung(29)|ovary(3)|pancreas(1)|prostate(2)|skin(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	77	all_cancers(12;0.000673)	Lung NSC(34;0.0205)|all_lung(34;0.0264)				TTCAGGAGGTCGAGTTGTGTC	0.443													C|||	83	0.0165735	0.0	0.0	5008	,	,		17760	0.0823		0.0	False		,,,				2504	0.0				p.V403V		Atlas-SNP	.											.	PDZRN4	346	.	0			c.C1209T						PASS	.	C	,	0,4406		0,0,2203	161.0	143.0	149.0		1209,435	1.1	1.0	12	dbSNP_132	149	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	PDZRN4	NM_001164595.1,NM_013377.3	,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,	403/1037,145/779	41946463	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	29951	exon6			GGAGGTCGAGTTG	AK094690	CCDS8739.1, CCDS53777.1	12q12	2008-08-14	2008-08-14			ENSG00000165966		"""RING-type (C3HC4) zinc fingers"""	30552	protein-coding gene	gene with protein product	"""similar to semaF cytoplasmic domain associated protein 3"""	609730				11230166, 15010864	Standard	NM_013377		Approved	DKFZp434B0417, LNX4, FLJ33777, IMAGE5767589	uc010skn.2	Q6ZMN7		ENST00000402685.2:c.1209C>T	12.37:g.41946463C>T		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	58	4	0.0689655	NM_001164595	Q52LY3|Q52LY4|Q6N052|Q8IUU1|Q9NTP7	Silent	SNP	ENST00000402685.2	37	CCDS53777.1																																																																																			C|0.991;T|0.009	0.009	strong		0.443	PDZRN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403701.1	NM_013377	
MEGF10	84466	hgsc.bcm.edu	37	5	126674869	126674869	+	Silent	SNP	G	G	A	rs12654455	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr5:126674869G>A	ENST00000274473.6	+	4	441	c.174G>A	c.(172-174)acG>acA	p.T58T	MEGF10_ENST00000508365.1_Silent_p.T58T|MEGF10_ENST00000418761.2_Silent_p.T58T|MEGF10_ENST00000503335.2_Silent_p.T58T	NM_032446.2	NP_115822.1	Q96KG7	MEG10_HUMAN	multiple EGF-like-domains 10	58	EMI. {ECO:0000255|PROSITE- ProRule:PRU00384}.|Necessary for interaction with AP2M1, self-assembly and formation of the irregular, mosaic-like adhesion pattern.				homotypic cell-cell adhesion (GO:0034109)|muscle cell development (GO:0055001)|recognition of apoptotic cell (GO:0043654)|regulation of muscle cell differentiation (GO:0051147)|regulation of skeletal muscle tissue development (GO:0048641)|skeletal muscle satellite cell activation (GO:0014719)|skeletal muscle satellite cell differentiation (GO:0014816)|skeletal muscle satellite cell proliferation (GO:0014841)	cell projection (GO:0042995)|integral component of membrane (GO:0016021)|phagocytic cup (GO:0001891)				breast(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(28)|ovary(4)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	68		Prostate(80;0.165)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0657)|Epithelial(69;0.123)		TTTACTACACGAGCTGCACTG	0.383													g|||	237	0.0473243	0.0083	0.0086	5008	,	,		18088	0.0972		0.0159	False		,,,				2504	0.1084				p.T58T		Atlas-SNP	.											.	MEGF10	152	.	0			c.G174A						PASS	.	A		21,4385	28.1+/-56.4	0,21,2182	123.0	110.0	114.0		174	-11.8	0.1	5	dbSNP_120	114	105,8495	57.2+/-118.5	0,105,4195	no	coding-synonymous	MEGF10	NM_032446.2		0,126,6377	AA,AG,GG		1.2209,0.4766,0.9688		58/1141	126674869	126,12880	2203	4300	6503	SO:0001819	synonymous_variant	84466	exon4			CTACACGAGCTGC	AK021631	CCDS4142.1	5q33	2008-02-05			ENSG00000145794	ENSG00000145794			29634	protein-coding gene	gene with protein product		612453				11347906	Standard	NM_032446		Approved	KIAA1780	uc003kui.4	Q96KG7	OTTHUMG00000128984	ENST00000274473.6:c.174G>A	5.37:g.126674869G>A		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	98	4	0.0408163	NM_032446	Q68DE5|Q8WUL3	Silent	SNP	ENST00000274473.6	37	CCDS4142.1																																																																																			G|0.975;A|0.025	0.025	strong		0.383	MEGF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250973.2	NM_032446	
BRCA2	675	hgsc.bcm.edu	37	13	32906729	32906729	+	Missense_Mutation	SNP	A	A	C	rs144848	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr13:32906729A>C	ENST00000380152.3	+	10	1347	c.1114A>C	c.(1114-1116)Aat>Cat	p.N372H	BRCA2_ENST00000544455.1_Missense_Mutation_p.N372H			P51587	BRCA2_HUMAN	breast cancer 2, early onset	372			H -> N (common polymorphism; associated with an increased risk of breast cancer and with an effect on prenatal viability with increased fitness of males and decreased fitness of females; dbSNP:rs144848). {ECO:0000269|PubMed:10323242, ECO:0000269|PubMed:10978364, ECO:0000269|PubMed:11062481, ECO:0000269|PubMed:12552570, ECO:0000269|PubMed:15057823, ECO:0000269|PubMed:15172753, ECO:0000269|PubMed:15365993, ECO:0000269|PubMed:8665505, ECO:0000269|PubMed:8673091, ECO:0000269|Ref.3}.		brain development (GO:0007420)|cell aging (GO:0007569)|centrosome duplication (GO:0051298)|cytokinesis (GO:0000910)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|female gonad development (GO:0008585)|hemopoiesis (GO:0030097)|histone H3 acetylation (GO:0043966)|histone H4 acetylation (GO:0043967)|inner cell mass cell proliferation (GO:0001833)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|male meiosis I (GO:0007141)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|nucleotide-excision repair (GO:0006289)|oocyte maturation (GO:0001556)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokinesis (GO:0032465)|replication fork protection (GO:0048478)|response to gamma radiation (GO:0010332)|response to UV-C (GO:0010225)|response to X-ray (GO:0010165)|spermatogenesis (GO:0007283)	BRCA2-MAGE-D1 complex (GO:0033593)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|secretory granule (GO:0030141)	gamma-tubulin binding (GO:0043015)|H3 histone acetyltransferase activity (GO:0010484)|H4 histone acetyltransferase activity (GO:0010485)|protease binding (GO:0002020)|single-stranded DNA binding (GO:0003697)	p.N372H(1)		NS(3)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(32)|liver(1)|lung(41)|oesophagus(5)|ovary(22)|pancreas(4)|prostate(3)|salivary_gland(1)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	183		Lung SC(185;0.0262)		all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704)		AAATGTAGCAAATCAGAAGCC	0.373			"""D, Mis, N, F, S"""		"""breast, ovarian, pancreatic"""	"""breast, ovarian, pancreatic, leukemia  (FANCB, FANCD1)"""		Homologous recombination	Pancreatic Cancer, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Prostate Cancer;Hereditary Breast-Ovarian Cancer, BRCA2 type;Fanconi Anemia type D1, bi-allelic BRCA2 mutations;Fanconi Anemia	TCGA Ovarian(8;0.087)			A|||	1249	0.249401	0.084	0.2997	5008	,	,		17972	0.2847		0.2952	False		,,,				2504	0.3538				p.N372H	Esophageal Squamous(138;838 1285 7957 30353 30468 36915 49332)	Atlas-SNP	.	yes	Rec	yes	Hereditary breast/ovarian cancer	13	13q12	675	familial breast/ovarian cancer gene 2		"""L, E"""	BRCA2_ENST00000544455,NS,carcinoma,0,1	BRCA2	812	1	1	Substitution - Missense(1)	stomach(1)	c.A1114C	GRCh37	CM002750	BRCA2	M	rs144848	PASS	.	A	HIS/ASN	558,3770		42,474,1648	167.0	186.0	180.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1114	0.4	0.0	13	dbSNP_83	180	2449,6117		345,1759,2179	yes	missense	BRCA2	NM_000059.3	68	387,2233,3827	CC,CA,AA		28.5898,12.8928,23.3209	benign	372/3419	32906729	3007,9887	2164	4283	6447	SO:0001583	missense	675	exon10	Familial Cancer Database	incl.: Hereditary Pancreatic Adenocarcinoma, Insulin-Dependent Diabetes Mellitus - Exocrine Insufficiency - Familial Pancreatic Cancer, PNCA1;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;HPC; ;FANCD1;Pancytopenia Dysmelia, FA (several complementation groups)	GTAGCAAATCAGA	U43746	CCDS9344.1	13q12-q13	2014-09-17	2003-10-14		ENSG00000139618	ENSG00000139618		"""Fanconi anemia, complementation groups"""	1101	protein-coding gene	gene with protein product	"""BRCA1/BRCA2-containing complex, subunit 2"""	600185	"""Fanconi anemia, complementation group D1"""	FANCD1, FACD, FANCD		8091231, 7581463, 15057823	Standard	NM_000059		Approved	FAD, FAD1, BRCC2	uc001uub.1	P51587	OTTHUMG00000017411	ENST00000380152.3:c.1114A>C	13.37:g.32906729A>C	ENSP00000369497:p.Asn372His	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	80	4	0.05	NM_000059	O00183|O15008|Q13879|Q5TBJ7	Missense_Mutation	SNP	ENST00000380152.3	37	CCDS9344.1	525	0.2403846153846154	48	0.0975609756097561	113	0.31215469613259667	146	0.25524475524475526	218	0.287598944591029	A	6.228	0.410176	0.11812	0.128928	0.285898	ENSG00000139618	ENST00000380152;ENST00000544455;ENST00000530893	T;T	0.00717	5.79;5.79	5.6	0.396	0.16309	.	1.242150	0.05390	N	0.538920	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.41448	-0.9508	6	0.46703	T	0.11	.	5.256	0.15548	0.4454:0.162:0.3926:0.0	rs144848;rs703222;rs766172;rs17593227;rs52835869;rs60042381;rs144848	.	.	.	H	372;372;370	ENSP00000369497:N372H;ENSP00000439902:N372H	ENSP00000369497:N372H	N	+	1	0	BRCA2	31804729	0.001000	0.12720	0.000000	0.03702	0.316000	0.28119	0.757000	0.26433	-0.147000	0.11254	-0.250000	0.11733	AAT	T|0.005;G|0.003	.	strong		0.373	BRCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046000.2	NM_000059	
PIK3C3	5289	hgsc.bcm.edu	37	18	39617703	39617703	+	Silent	SNP	C	C	A	rs143493401	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr18:39617703C>A	ENST00000262039.4	+	17	1973	c.1887C>A	c.(1885-1887)ggC>ggA	p.G629G	PIK3C3_ENST00000589056.1_5'Flank|PIK3C3_ENST00000587402.1_5'Flank|PIK3C3_ENST00000398870.3_Silent_p.G566G|PIK3C3_ENST00000593098.1_Silent_p.G114G	NM_002647.2	NP_002638.2	Q8NEB9	PK3C3_HUMAN	phosphatidylinositol 3-kinase, catalytic subunit type 3	629					autophagic vacuole assembly (GO:0000045)|cytokinesis (GO:0000910)|early endosome to late endosome transport (GO:0045022)|endosome organization (GO:0007032)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|protein processing (GO:0016485)|regulation of protein secretion (GO:0050708)|response to leucine (GO:0043201)|small molecule metabolic process (GO:0044281)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)	axoneme (GO:0005930)|cytosol (GO:0005829)|late endosome (GO:0005770)|membrane (GO:0016020)|midbody (GO:0030496)|phagocytic vesicle (GO:0045335)|phosphatidylinositol 3-kinase complex (GO:0005942)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|ATP binding (GO:0005524)|protein kinase activity (GO:0004672)			breast(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(10)|liver(1)|lung(25)|ovary(1)|skin(2)|urinary_tract(1)	49						AAGATGGAGGCAAATATCCAG	0.333										TSP Lung(28;0.18)			C|||	61	0.0121805	0.0	0.0677	5008	,	,		19118	0.0119		0.0	False		,,,				2504	0.002				p.G629G	NSCLC(37;552 1060 2683 16430 37914)	Atlas-SNP	.											PIK3C3,lower_third,carcinoma,+1,1	PIK3C3	138	1	0			c.C1887A						scavenged	.	C		0,4406		0,0,2203	161.0	153.0	156.0		1887	3.9	1.0	18	dbSNP_134	156	2,8598	1.2+/-3.3	0,2,4298	no	coding-synonymous	PIK3C3	NM_002647.2		0,2,6501	AA,AC,CC		0.0233,0.0,0.0154		629/888	39617703	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	5289	exon17			TGGAGGCAAATAT	Z46973	CCDS11920.1	18q12.3	2012-07-13	2012-07-13		ENSG00000078142	ENSG00000078142	2.7.1.137		8974	protein-coding gene	gene with protein product		602609	"""phosphoinositide-3-kinase, class 3"""			7628435	Standard	NM_002647		Approved	Vps34	uc002lap.3	Q8NEB9	OTTHUMG00000132593	ENST00000262039.4:c.1887C>A	18.37:g.39617703C>A		Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	107	4	0.0373832	NM_002647	Q15134	Silent	SNP	ENST00000262039.4	37	CCDS11920.1																																																																																			C|0.994;A|0.006	0.006	strong		0.333	PIK3C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255804.1	NM_002647	
TYW1	55253	hgsc.bcm.edu	37	7	66479413	66479413	+	Silent	SNP	T	T	C			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr7:66479413T>C	ENST00000359626.5	+	5	599	c.435T>C	c.(433-435)acT>acC	p.T145T		NM_018264.2	NP_060734.2	Q9NV66	TYW1_HUMAN	tRNA-yW synthesizing protein 1 homolog (S. cerevisiae)	145	Flavodoxin-like. {ECO:0000255|PROSITE- ProRule:PRU00088}.				tRNA processing (GO:0008033)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|FMN binding (GO:0010181)|iron ion binding (GO:0005506)|lyase activity (GO:0016829)|oxidoreductase activity (GO:0016491)	p.T145T(1)		breast(1)|endometrium(8)|kidney(10)|large_intestine(4)|lung(13)|ovary(1)|prostate(2)|skin(3)|stomach(2)|urinary_tract(2)	46		Lung NSC(55;0.0846)|all_lung(88;0.183)				GCCTACCAACTGAAAGTGCAG	0.428																																					p.T145T		Atlas-SNP	.											TYW1,NS,carcinoma,0,1	TYW1	71	1	1	Substitution - coding silent(1)	urinary_tract(1)	c.T435C						scavenged	.																																			SO:0001819	synonymous_variant	55253	exon5			ACCAACTGAAAGT	AK001762	CCDS5538.1	7q11.21	2007-11-29	2007-11-29	2007-11-29	ENSG00000198874	ENSG00000198874			25598	protein-coding gene	gene with protein product	"""tRNA-yW synthesizing protein 1 homolog A (S. cerevisiae)"""	611243	"""radical S-adenosyl methionine and flavodoxin domains 1"""	RSAFD1		16162496, 17150819	Standard	NM_018264		Approved	FLJ10900, MGC23001, MGC60291, YPL207W, TYW1A	uc003tvn.4	Q9NV66	OTTHUMG00000129723	ENST00000359626.5:c.435T>C	7.37:g.66479413T>C		Somatic	301	0	0		WXS	Illumina HiSeq	Phase_I	275	4	0.0145455	NM_018264	Q6PJG8|Q75MG8|Q75MN3|Q86V12|Q8IVS7|Q9H9C4	Silent	SNP	ENST00000359626.5	37	CCDS5538.1																																																																																			.	.	weak		0.428	TYW1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251932.2	NM_018264	
KCNH2	3757	hgsc.bcm.edu	37	7	150648789	150648789	+	Silent	SNP	T	T	C	rs1805121	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr7:150648789T>C	ENST00000262186.5	-	7	2093	c.1692A>G	c.(1690-1692)ctA>ctG	p.L564L	KCNH2_ENST00000392968.2_Silent_p.L468L|KCNH2_ENST00000330883.4_Silent_p.L224L|KCNH2_ENST00000430723.3_Silent_p.L564L	NM_000238.3	NP_000229.1	Q12809	KCNH2_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 2	564			L -> P (in LQT2).		cardiac muscle contraction (GO:0060048)|cellular response to drug (GO:0035690)|membrane depolarization during action potential (GO:0086010)|membrane repolarization during action potential (GO:0086011)|membrane repolarization during cardiac muscle cell action potential (GO:0086013)|negative regulation of potassium ion export (GO:1902303)|negative regulation of potassium ion transmembrane transport (GO:1901380)|positive regulation of potassium ion transmembrane transport (GO:1901381)|potassium ion export (GO:0071435)|potassium ion homeostasis (GO:0055075)|potassium ion transmembrane transport (GO:0071805)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of heart rate by hormone (GO:0003064)|regulation of membrane potential (GO:0042391)|regulation of membrane repolarization (GO:0060306)|regulation of potassium ion transmembrane transport (GO:1901379)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|synaptic transmission (GO:0007268)|ventricular cardiac muscle cell action potential (GO:0086005)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|identical protein binding (GO:0042802)|inward rectifier potassium channel activity (GO:0005242)|phosphorelay sensor kinase activity (GO:0000155)|protein homodimerization activity (GO:0042803)|ubiquitin protein ligase binding (GO:0031625)|voltage-gated potassium channel activity (GO:0005249)|voltage-gated potassium channel activity involved in ventricular cardiac muscle cell action potential repolarization (GO:1902282)			NS(1)|cervix(1)|endometrium(10)|kidney(1)|large_intestine(5)|lung(14)|ovary(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)	42	all_neural(206;0.219)		OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)	Alfuzosin(DB00346)|Amiodarone(DB01118)|Amsacrine(DB00276)|Astemizole(DB00637)|Carvedilol(DB01136)|Chlorpromazine(DB00477)|Cisapride(DB00604)|Dofetilide(DB00204)|Doxazosin(DB00590)|Doxepin(DB01142)|Dronedarone(DB04855)|Halofantrine(DB01218)|Ibutilide(DB00308)|Imipramine(DB00458)|Miconazole(DB01110)|Pimozide(DB01100)|Prazosin(DB00457)|Propafenone(DB01182)|Quinidine(DB00908)|Sertindole(DB06144)|Sotalol(DB00489)|Terazosin(DB01162)|Thioridazine(DB00679)|Verapamil(DB00661)	AGATGCAGGCTAGCCAGTGCG	0.622													C|||	3047	0.608427	0.82	0.4625	5008	,	,		17035	0.8343		0.3608	False		,,,				2504	0.4479				p.L564L	GBM(137;110 1844 13671 20123 45161)	Atlas-SNP	.											KCNH2_ENST00000430723,NS,carcinoma,0,2	KCNH2	157	2	0			c.A1692G						PASS	.	C	,,,	3268,1138	406.2+/-333.8	1230,808,165	75.0	61.0	65.0		1692,672,1692,672	3.5	1.0	7	dbSNP_89	65	3097,5503	658.0+/-401.5	588,1921,1791	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	KCNH2	NM_000238.3,NM_001204798.1,NM_172056.2,NM_172057.2	,,,	1818,2729,1956	CC,CT,TT		36.0116,25.8284,48.939	,,,	564/1160,224/549,564/889,224/820	150648789	6365,6641	2203	4300	6503	SO:0001819	synonymous_variant	3757	exon7			GCAGGCTAGCCAG	U04270	CCDS5910.1, CCDS5911.1	7q36.1	2014-09-17			ENSG00000055118	ENSG00000055118		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6251	protein-coding gene	gene with protein product		152427		LQT2		18616963, 7842012, 8159766, 16382104	Standard	NM_000238		Approved	Kv11.1, HERG, erg1	uc003wic.3	Q12809	OTTHUMG00000158341	ENST00000262186.5:c.1692A>G	7.37:g.150648789T>C		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	96	5	0.0520833	NM_000238	A5H1P7|C4PFH9|D3DX04|O75418|O75680|Q708S9|Q9BT72|Q9BUT7|Q9H3P0	Silent	SNP	ENST00000262186.5	37	CCDS5910.1																																																																																			T|0.477;C|0.523	0.523	strong		0.622	KCNH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350741.2	NM_000238	
FOLH1	2346	hgsc.bcm.edu	37	11	49204779	49204779	+	Missense_Mutation	SNP	C	C	T	rs116795343	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr11:49204779C>T	ENST00000256999.2	-	7	1102	c.842G>A	c.(841-843)cGt>cAt	p.R281H	FOLH1_ENST00000356696.3_Missense_Mutation_p.R281H|FOLH1_ENST00000533034.1_Missense_Mutation_p.R266H|FOLH1_ENST00000343844.4_De_novo_Start_OutOfFrame|FOLH1_ENST00000340334.7_Missense_Mutation_p.R266H	NM_004476.1	NP_004467.1	Q04609	FOLH1_HUMAN	folate hydrolase (prostate-specific membrane antigen) 1	281	NAALADase.				folic acid-containing compound metabolic process (GO:0006760)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	carboxypeptidase activity (GO:0004180)|dipeptidase activity (GO:0016805)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|peptidase activity (GO:0008233)	p.R281L(1)		NS(2)|breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(7)|lung(34)|ovary(1)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	60					Capromab(DB00089)	TGCAATTCCACGCCTATAAGC	0.348																																					p.R281H		Atlas-SNP	.											FOLH1,NS,carcinoma,-1,2	FOLH1	141	2	1	Substitution - Missense(1)	lung(1)	c.G842A						scavenged	.						72.0	73.0	73.0					11																	49204779		2201	4298	6499	SO:0001583	missense	2346	exon7			ATTCCACGCCTAT	M99487	CCDS7946.1, CCDS31493.1, CCDS53626.1, CCDS53627.1, CCDS53628.1	11p11.2	2011-07-22			ENSG00000086205	ENSG00000086205	3.4.17.21		3788	protein-coding gene	gene with protein product	"""glutamate carboxylase II"", ""glutamate carboxypeptidase II"""	600934		FOLH		9838072	Standard	NM_001193472		Approved	PSM, PSMA, NAALAD1, NAALAdase, GCP2, GCPII	uc001ngy.3	Q04609	OTTHUMG00000166625	ENST00000256999.2:c.842G>A	11.37:g.49204779C>T	ENSP00000256999:p.Arg281His	Somatic	240	2	0.00833333		WXS	Illumina HiSeq	Phase_I	300	7	0.0233333	NM_004476	A4UU12|A9CB79|B7Z312|B7Z343|D3DQS5|E9PDX8|O43748|Q16305|Q541A4|Q8TAY3|Q9NP15|Q9NYE2|Q9P1P8	Missense_Mutation	SNP	ENST00000256999.2	37	CCDS7946.1	.	.	.	.	.	.	.	.	.	.	C	2.929	-0.221410	0.06061	.	.	ENSG00000086205	ENST00000256999;ENST00000356696;ENST00000340334;ENST00000533034;ENST00000389724	T;T;T;T	0.43294	0.95;0.95;0.95;0.95	2.76	-1.12	0.09808	.	0.978445	0.08346	N	0.960084	T	0.21427	0.0516	N	0.14661	0.345	0.80722	D	1	B;B;B;B	0.06786	0.001;0.001;0.0;0.0	B;B;B;B	0.06405	0.001;0.0;0.002;0.0	T	0.23655	-1.0182	10	0.14656	T	0.56	.	6.6038	0.22714	0.0:0.3193:0.0:0.6807	.	266;266;281;281	Q04609-9;Q04609-7;Q04609-8;Q04609	.;.;.;FOLH1_HUMAN	H	281;281;266;266;281	ENSP00000256999:R281H;ENSP00000349129:R281H;ENSP00000344131:R266H;ENSP00000431463:R266H	ENSP00000256999:R281H	R	-	2	0	FOLH1	49161355	0.002000	0.14202	0.792000	0.32020	0.272000	0.26649	-0.922000	0.04004	-0.085000	0.12573	0.194000	0.17425	CGT	C|0.974;T|0.026	0.026	strong		0.348	FOLH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390896.1	NM_004476	
C6orf15	29113	hgsc.bcm.edu	37	6	31079894	31079894	+	Missense_Mutation	SNP	A	A	G	rs2233977	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr6:31079894A>G	ENST00000259870.3	-	2	245	c.242T>C	c.(241-243)gTg>gCg	p.V81A	PSORS1C1_ENST00000259881.9_5'Flank	NM_014070.2	NP_054789.2	Q6UXA7	CF015_HUMAN	chromosome 6 open reading frame 15	81			V -> A (in dbSNP:rs2233977).		extracellular matrix organization (GO:0030198)	interstitial matrix (GO:0005614)	heparin binding (GO:0008201)|hyaluronic acid binding (GO:0005540)			endometrium(3)|large_intestine(2)|lung(9)|prostate(1)|skin(1)|stomach(1)	17						TGATGCAGGCACGCTGAGCTT	0.607													G|||	1071	0.213858	0.087	0.1974	5008	,	,		16805	0.3899		0.169	False		,,,				2504	0.2618				p.V81A		Atlas-SNP	.											C6orf15,NS,carcinoma,-1,1	C6orf15	29	1	0			c.T242C						scavenged	.	G	ALA/VAL	464,3942	764.3+/-413.3	21,422,1760	61.0	67.0	65.0		242	-8.4	0.0	6	dbSNP_98	65	1456,7144	744.7+/-407.2	131,1194,2975	yes	missense	C6orf15	NM_014070.2	64	152,1616,4735	GG,GA,AA		16.9302,10.5311,14.7624	benign	81/326	31079894	1920,11086	2203	4300	6503	SO:0001583	missense	29113	exon2			GCAGGCACGCTGA	AB031481	CCDS4693.1	6p21	2011-12-12			ENSG00000204542	ENSG00000204542			13927	protein-coding gene	gene with protein product		611401					Standard	NM_014070		Approved	STG	uc003nsk.1	Q6UXA7	OTTHUMG00000031111	ENST00000259870.3:c.242T>C	6.37:g.31079894A>G	ENSP00000259870:p.Val81Ala	Somatic	85	1	0.0117647		WXS	Illumina HiSeq	Phase_I	90	4	0.0444444	NM_014070	B0S7V8|Q0EFA6|Q2L6G7|Q5SQ81|Q86Z05|Q9UIG3	Missense_Mutation	SNP	ENST00000259870.3	37	CCDS4693.1	458	0.2097069597069597	53	0.10772357723577236	54	0.14917127071823205	222	0.3881118881118881	129	0.17018469656992086	G	1.094	-0.663129	0.03428	0.105311	0.169302	ENSG00000204542	ENST00000259870	T	0.05025	3.51	4.61	-8.37	0.00976	.	1.975560	0.02836	N	0.127304	T	0.00412	0.0013	N	0.01267	-0.92	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.40515	-0.9559	9	0.07644	T	0.81	-15.0007	5.3978	0.16278	0.3695:0.0:0.2882:0.3423	rs2233977;rs2233977	81	Q6UXA7	CF015_HUMAN	A	81	ENSP00000259870:V81A	ENSP00000259870:V81A	V	-	2	0	C6orf15	31187873	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.201000	0.01236	-2.546000	0.00482	-1.841000	0.00585	GTG	A|0.825;G|0.175	0.175	strong		0.607	C6orf15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076184.2	NM_014070	
SYMPK	8189	hgsc.bcm.edu	37	19	46330809	46330809	+	Silent	SNP	G	G	A	rs35490979	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr19:46330809G>A	ENST00000245934.7	-	16	2384	c.2140C>T	c.(2140-2142)Ctg>Ttg	p.L714L	AC092301.3_ENST00000601618.1_RNA	NM_004819.2	NP_004810.2	Q92797	SYMPK_HUMAN	symplekin	714					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)		AGGACATGCAGGTACTGGAAC	0.602													G|||	551	0.110024	0.0772	0.0331	5008	,	,		18904	0.3512		0.0358	False		,,,				2504	0.0368				p.L714L		Atlas-SNP	.											.	SYMPK	104	.	0			c.C2140T						PASS	.	G		261,4145	148.8+/-183.1	6,249,1948	122.0	90.0	101.0		2140	2.8	1.0	19	dbSNP_126	101	277,8323	104.8+/-165.8	5,267,4028	no	coding-synonymous	SYMPK	NM_004819.2		11,516,5976	AA,AG,GG		3.2209,5.9237,4.1366		714/1275	46330809	538,12468	2203	4300	6503	SO:0001819	synonymous_variant	8189	exon16			CATGCAGGTACTG	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.2140C>T	19.37:g.46330809G>A		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	106	5	0.0471698	NM_004819	O00521|O00689|O00733|Q59GT5|Q8N2U5	Silent	SNP	ENST00000245934.7	37	CCDS12676.2	293	0.13415750915750915	34	0.06910569105691057	14	0.03867403314917127	222	0.3881118881118881	23	0.030343007915567283	G	10.07	1.248643	0.22880	0.059237	0.032209	ENSG00000125755	ENST00000340643	.	.	.	4.93	2.78	0.32641	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.41538	-0.9503	3	.	.	.	.	9.4228	0.38561	0.1745:0.0:0.8255:0.0	rs35490979	.	.	.	L	145	.	.	P	-	2	0	SYMPK	51022649	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	3.448000	0.52943	0.681000	0.31386	0.650000	0.86243	CCT	G|0.931;A|0.069	0.069	strong		0.602	SYMPK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316581.1	NM_004819	
GPR152	390212	hgsc.bcm.edu	37	11	67220015	67220015	+	Missense_Mutation	SNP	C	C	T	rs79423227	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr11:67220015C>T	ENST00000312457.2	-	1	185	c.181G>A	c.(181-183)Gga>Aga	p.G61R	CABP4_ENST00000542025.2_3'UTR|CABP4_ENST00000438189.2_5'UTR|CABP4_ENST00000325656.5_5'Flank	NM_206997.1	NP_996880.1	Q8TDT2	GP152_HUMAN	G protein-coupled receptor 152	61						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(7)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	16			BRCA - Breast invasive adenocarcinoma(15;8.18e-06)			GTGCCAGCTCCATGCCGGGCC	0.667													C|||	189	0.0377396	0.0015	0.013	5008	,	,		17001	0.1677		0.002	False		,,,				2504	0.0072				p.G61R	Pancreas(102;800 1581 2723 7382 33622)	Atlas-SNP	.											.	GPR152	41	.	0			c.G181A						PASS	.	C	ARG/GLY	8,4384		0,8,2188	18.0	19.0	19.0		181	4.0	0.3	11	dbSNP_131	19	8,8574		0,8,4283	yes	missense	GPR152	NM_206997.1	125	0,16,6471	TT,TC,CC		0.0932,0.1821,0.1233	benign	61/471	67220015	16,12958	2196	4291	6487	SO:0001583	missense	390212	exon1			CAGCTCCATGCCG	AY255600	CCDS8165.1	11q13.2	2013-09-20			ENSG00000175514	ENSG00000175514		"""GPCR / Class A : Orphans"""	23622	protein-coding gene	gene with protein product						12679517	Standard	NM_206997		Approved	PGR5	uc001olm.3	Q8TDT2	OTTHUMG00000168032	ENST00000312457.2:c.181G>A	11.37:g.67220015C>T	ENSP00000310255:p.Gly61Arg	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	139	6	0.0431655	NM_206997	Q0VD88|Q86SM0	Missense_Mutation	SNP	ENST00000312457.2	37	CCDS8165.1	118	0.05402930402930403	1	0.0020325203252032522	4	0.011049723756906077	110	0.19230769230769232	3	0.00395778364116095	C	12.65	2.002504	0.35320	0.001821	9.32E-4	ENSG00000175514	ENST00000312457	T	0.29655	1.56	5.01	4.02	0.46733	GPCR, rhodopsin-like superfamily (1);	0.184672	0.26311	N	0.025110	T	0.00012	0.0000	N	0.00841	-1.15	0.40787	P	0.016773000000000038	B	0.33694	0.421	B	0.36808	0.233	T	0.22836	-1.0205	9	0.14252	T	0.57	.	5.59	0.17295	0.0:0.6866:0.2043:0.1091	.	61	Q8TDT2	GP152_HUMAN	R	61	ENSP00000310255:G61R	ENSP00000310255:G61R	G	-	1	0	GPR152	66976591	0.000000	0.05858	0.314000	0.25224	0.209000	0.24338	0.371000	0.20450	2.599000	0.87857	0.561000	0.74099	GGA	C|0.975;T|0.025	0.025	strong		0.667	GPR152-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397623.1		
GDE1	51573	hgsc.bcm.edu	37	16	19516398	19516398	+	Missense_Mutation	SNP	C	C	T	rs2072086	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr16:19516398C>T	ENST00000353258.3	-	5	833	c.653G>A	c.(652-654)cGg>cAg	p.R218Q	CTA-363E6.7_ENST00000569345.1_RNA	NM_016641.3	NP_057725.1	Q9NZC3	GDE1_HUMAN	glycerophosphodiester phosphodiesterase 1	218	GP-PDE.		R -> Q (in dbSNP:rs2072086).		glycerol metabolic process (GO:0006071)|lipid metabolic process (GO:0006629)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)	glycerophosphodiester phosphodiesterase activity (GO:0008889)|glycerophosphoinositol glycerophosphodiesterase activity (GO:0047395)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(6)|ovary(2)|prostate(1)	13						TATTACATCCCGATCTGTTTG	0.353													C|||	14	0.00279553	0.0	0.0	5008	,	,		20236	0.0139		0.0	False		,,,				2504	0.0				p.R218Q		Atlas-SNP	.											GDE1,caecum,carcinoma,-1,2	GDE1	31	2	0			c.G653A						scavenged	.	C	GLN/ARG	1,4393	2.1+/-5.4	0,1,2196	184.0	179.0	180.0		653	-2.8	0.2	16	dbSNP_96	180	0,8600		0,0,4300	yes	missense	GDE1	NM_016641.3	43	0,1,6496	TT,TC,CC		0.0,0.0228,0.0077	benign	218/332	19516398	1,12993	2197	4300	6497	SO:0001583	missense	51573	exon5			ACATCCCGATCTG		CCDS10578.1	16p12-p11.2	2011-01-25			ENSG00000006007	ENSG00000006007	3.1.4.46		29644	protein-coding gene	gene with protein product	"""membrane interacting protein of RGS16"""	605943				12576545, 16472945	Standard	NM_016641		Approved	MIR16	uc002dgh.3	Q9NZC3	OTTHUMG00000131454	ENST00000353258.3:c.653G>A	16.37:g.19516398C>T	ENSP00000261386:p.Arg218Gln	Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	165	4	0.0242424	NM_016641	O43334|Q6PKF7|Q7KYR4	Missense_Mutation	SNP	ENST00000353258.3	37	CCDS10578.1	14	0.00641025641025641	0	0.0	0	0.0	14	0.024475524475524476	0	0.0	C	8.757	0.922737	0.18056	2.28E-4	0.0	ENSG00000006007	ENST00000353258	T	0.11277	2.79	5.66	-2.78	0.05859	PLC-like phosphodiesterase, TIM beta/alpha-barrel domain (2);	0.504521	0.22467	N	0.059671	T	0.02533	0.0077	N	0.19112	0.55	0.28069	N	0.932669	B	0.11235	0.004	B	0.09377	0.004	T	0.25606	-1.0127	10	0.40728	T	0.16	-0.5592	9.2607	0.37610	0.0:0.5814:0.1267:0.2919	rs2072086;rs2072086	218	Q9NZC3	GDE1_HUMAN	Q	218	ENSP00000261386:R218Q	ENSP00000261386:R218Q	R	-	2	0	GDE1	19423899	0.998000	0.40836	0.190000	0.23270	0.316000	0.28119	1.481000	0.35476	-0.401000	0.07644	-1.261000	0.01458	CGG	C|0.996;T|0.004	0.004	strong		0.353	GDE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254274.2	NM_016641	
ACSM2A	123876	hgsc.bcm.edu	37	16	20494408	20494408	+	Missense_Mutation	SNP	C	C	T	rs1133607	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr16:20494408C>T	ENST00000573854.1	+	13	1652	c.1538C>T	c.(1537-1539)tCg>tTg	p.S513L	ACSM2A_ENST00000575690.1_Missense_Mutation_p.S513L|ACSM2A_ENST00000536134.1_Missense_Mutation_p.S285L|ACSM2A_ENST00000219054.6_Missense_Mutation_p.S513L|ACSM2A_ENST00000417235.2_Missense_Mutation_p.S434L|ACSM2A_ENST00000396104.2_Missense_Mutation_p.S513L	NM_001010845.2	NP_001010845	Q08AH3	ACS2A_HUMAN	acyl-CoA synthetase medium-chain family member 2A	513			S -> L (in dbSNP:rs1133607). {ECO:0000269|PubMed:10493829, ECO:0000269|PubMed:12654705, ECO:0000269|PubMed:16521160}.		fatty acid metabolic process (GO:0006631)|glucose homeostasis (GO:0042593)|medium-chain fatty-acyl-CoA metabolic process (GO:0036112)|triglyceride homeostasis (GO:0070328)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|butyrate-CoA ligase activity (GO:0047760)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(34)|ovary(1)|skin(6)|stomach(1)	51						GTCCTGGCCTCGCAGTTCCTG	0.502													c|||	705	0.140775	0.1301	0.1369	5008	,	,		17954	0.1984		0.0746	False		,,,				2504	0.1667				p.S513L		Atlas-SNP	.											ACSM2A,NS,carcinoma,+1,1	ACSM2A	120	1	0			c.C1538T						scavenged	.	C	LEU/SER	551,3855	250.0+/-257.2	33,485,1685	199.0	178.0	185.0		1538	3.3	1.0	16	dbSNP_86	185	872,7728	197.6+/-242.2	31,810,3459	no	missense	ACSM2A	NM_001010845.2	145	64,1295,5144	TT,TC,CC		10.1395,12.5057,10.9411	benign	513/578	20494408	1423,11583	2203	4300	6503	SO:0001583	missense	123876	exon14			TGGCCTCGCAGTT	AK091878, AK096039	CCDS32401.1	16p12.3	2014-08-08	2007-06-20	2007-06-20	ENSG00000183747	ENSG00000183747		"""Acyl-CoA synthetase family"""	32017	protein-coding gene	gene with protein product		614358	"""acyl-CoA synthetase medium-chain family member 2"""	ACSM2			Standard	NM_001010845		Approved	A-923A4.1, MGC150530	uc010bwe.3	Q08AH3	OTTHUMG00000177401	ENST00000573854.1:c.1538C>T	16.37:g.20494408C>T	ENSP00000459451:p.Ser513Leu	Somatic	117	1	0.00854701		WXS	Illumina HiSeq	Phase_I	117	6	0.0512821	NM_001010845	B3KTT9|O75202	Missense_Mutation	SNP	ENST00000573854.1	37	CCDS32401.1	312	0.14285714285714285	74	0.15040650406504066	52	0.143646408839779	115	0.20104895104895104	71	0.09366754617414248	C	14.03	2.414161	0.42817	0.125057	0.101395	ENSG00000183747	ENST00000417235;ENST00000219054;ENST00000536134;ENST00000396104	T;T;T;T	0.51071	0.72;0.72;0.72;0.72	3.26	3.26	0.37387	.	0.461328	0.18403	N	0.142287	T	0.00073	0.0002	L	0.51914	1.62	0.09310	P	0.999999999999518	B	0.06786	0.001	B	0.04013	0.001	T	0.13415	-1.0510	9	0.66056	D	0.02	-0.9891	14.417	0.67158	0.0:1.0:0.0:0.0	rs1133607;rs1634313;rs3195484;rs16970281;rs52800134;rs1133607	513	Q08AH3	ACS2A_HUMAN	L	434;513;285;513	ENSP00000392169:S434L;ENSP00000219054:S513L;ENSP00000445082:S285L;ENSP00000379411:S513L	ENSP00000219054:S513L	S	+	2	0	ACSM2A	20401909	0.171000	0.23029	0.987000	0.45799	0.913000	0.54294	4.507000	0.60434	1.507000	0.48752	0.305000	0.20034	TCG	C|0.880;T|0.120	0.120	strong		0.502	ACSM2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436764.1	NM_001010845	
SLC45A2	51151	hgsc.bcm.edu	37	5	33963870	33963870	+	Missense_Mutation	SNP	C	C	T	rs26722	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr5:33963870C>T	ENST00000296589.4	-	3	960	c.814G>A	c.(814-816)Gag>Aag	p.E272K	SLC45A2_ENST00000509381.1_Intron|SLC45A2_ENST00000382102.3_Missense_Mutation_p.E272K|SLC45A2_ENST00000342059.3_Missense_Mutation_p.E213K|SLC45A2_ENST00000345083.5_Intron	NM_016180.3	NP_057264	Q9UMX9	S45A2_HUMAN	solute carrier family 45, member 2	272			E -> K (associated with SHEP5; significantly associated with dark hair, skin and eye color in Caucasians; dbSNP:rs26722). {ECO:0000269|PubMed:14722913, ECO:0000269|PubMed:14961451, ECO:0000269|PubMed:15455243, ECO:0000269|PubMed:15714523, ECO:0000269|PubMed:17768386}.		developmental pigmentation (GO:0048066)|melanin biosynthetic process (GO:0042438)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)				breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(25)|ovary(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	48						TTAACTTTCTCGATAGAACCA	0.433													C|||	892	0.178115	0.0439	0.3084	5008	,	,		19696	0.3909		0.0239	False		,,,				2504	0.2065				p.E272K	Ovarian(31;380 859 8490 22203 49048)	Atlas-SNP	.											.	SLC45A2	100	.	0			c.G814A	GRCh37	CM051555	SLC45A2	M	rs26722	PASS	.	C	LYS/GLU,LYS/GLU	219,4187	132.5+/-169.0	7,205,1991	157.0	162.0	160.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	814,814	2.1	0.4	5	dbSNP_76	160	145,8455	71.3+/-133.9	3,139,4158	yes	missense,missense	SLC45A2	NM_001012509.2,NM_016180.3	56,56	10,344,6149	TT,TC,CC		1.686,4.9705,2.7987	benign,benign	272/461,272/531	33963870	364,12642	2203	4300	6503	SO:0001583	missense	51151	exon3			CTTTCTCGATAGA	AF172849	CCDS3901.1, CCDS43308.1, CCDS75232.1	5p13.3	2013-08-06	2005-10-06	2005-10-06	ENSG00000164175	ENSG00000164175		"""Solute carriers"""	16472	protein-coding gene	gene with protein product		606202	"""membrane associated transporter"""	MATP		11916009, 11574907	Standard	NM_001012509		Approved	AIM-1, OCA4	uc003jid.3	Q9UMX9	OTTHUMG00000090719	ENST00000296589.4:c.814G>A	5.37:g.33963870C>T	ENSP00000296589:p.Glu272Lys	Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	113	6	0.0530973	NM_016180	Q6P2P0|Q9BTM3	Missense_Mutation	SNP	ENST00000296589.4	37	CCDS3901.1	340	0.15567765567765568	24	0.04878048780487805	84	0.23204419889502761	225	0.39335664335664333	7	0.009234828496042216	C	11.06	1.527052	0.27299	0.049705	0.01686	ENSG00000164175	ENST00000296589;ENST00000342059;ENST00000382102;ENST00000510600	D;T;D;D	0.93488	-3.23;2.29;-3.23;-3.23	5.83	2.14	0.27477	Major facilitator superfamily domain, general substrate transporter (1);	0.582555	0.19089	N	0.123023	T	0.00012	0.0000	L	0.40543	1.245	0.09310	P	0.999994897	B;B	0.12630	0.006;0.003	B;B	0.13407	0.006;0.009	T	0.08027	-1.0742	9	0.06891	T	0.86	-7.1423	9.8671	0.41150	0.0:0.7203:0.0:0.2797	rs26722;rs16892026;rs52832300;rs60285050;rs26722	272;272	Q9UMX9-4;Q9UMX9	.;S45A2_HUMAN	K	272;213;272;97	ENSP00000296589:E272K;ENSP00000341014:E213K;ENSP00000371534:E272K;ENSP00000424010:E97K	ENSP00000296589:E272K	E	-	1	0	SLC45A2	33999627	0.923000	0.31300	0.441000	0.26858	0.319000	0.28217	1.765000	0.38481	0.112000	0.17975	-1.012000	0.02466	GAG	C|0.910;T|0.090	0.090	strong		0.433	SLC45A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207443.2	NM_016180	
FAM131C	348487	hgsc.bcm.edu	37	1	16385184	16385184	+	Silent	SNP	G	G	A	rs75273615	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr1:16385184G>A	ENST00000375662.4	-	7	774	c.591C>T	c.(589-591)agC>agT	p.S197S	FAM131C_ENST00000494078.1_5'UTR	NM_182623.2	NP_872429.2	Q96AQ9	F131C_HUMAN	family with sequence similarity 131, member C	197								p.S197S(1)		large_intestine(2)|lung(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	8		Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Colorectal(212;8.32e-08)|COAD - Colon adenocarcinoma(227;5.56e-06)|BRCA - Breast invasive adenocarcinoma(304;9.12e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.00656)|READ - Rectum adenocarcinoma(331;0.0649)		CGCTGGGAAGGCTGTCCTGAA	0.642																																					p.S197S		Atlas-SNP	.											FAM131C,NS,haematopoietic_neoplasm,0,1	FAM131C	21	1	1	Substitution - coding silent(1)	lung(1)	c.C591T						scavenged	.						20.0	20.0	20.0					1																	16385184		2002	4131	6133	SO:0001819	synonymous_variant	348487	exon7			GGGAAGGCTGTCC		CCDS41270.1	1p36.13	2008-02-05	2007-03-20	2007-03-20	ENSG00000185519	ENSG00000185519			26717	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 117"""	C1orf117		12477932	Standard	NM_182623		Approved	FLJ36766	uc001axz.4	Q96AQ9	OTTHUMG00000009525	ENST00000375662.4:c.591C>T	1.37:g.16385184G>A		Somatic	380	2	0.00526316		WXS	Illumina HiSeq	Phase_I	434	7	0.016129	NM_182623	Q5T5Q5|Q8N3X3|Q8N9P9	Silent	SNP	ENST00000375662.4	37	CCDS41270.1																																																																																			G|0.740;A|0.260	0.260	strong		0.642	FAM131C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026319.1	NM_182623	
SH3BP4	23677	hgsc.bcm.edu	37	2	235951819	235951819	+	Silent	SNP	A	A	G	rs3795962	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr2:235951819A>G	ENST00000409212.1	+	4	2913	c.2406A>G	c.(2404-2406)ctA>ctG	p.L802L	SH3BP4_ENST00000392011.2_Silent_p.L802L|SH3BP4_ENST00000344528.4_Silent_p.L802L			Q9P0V3	SH3B4_HUMAN	SH3-domain binding protein 4	802					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)	p.L802L(1)		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)		CGTCCGTCCTAGAAAAGCTGA	0.587													G|||	3767	0.752196	0.9576	0.6499	5008	,	,		22177	0.9157		0.4612	False		,,,				2504	0.6779				p.L802L		Atlas-SNP	.											SH3BP4,NS,carcinoma,0,1	SH3BP4	109	1	1	Substitution - coding silent(1)	prostate(1)	c.A2406G						PASS	.	G		3881,525	224.3+/-240.5	1716,449,38	46.0	46.0	46.0		2406	2.0	1.0	2	dbSNP_107	46	3994,4606	566.4+/-388.7	926,2142,1232	no	coding-synonymous	SH3BP4	NM_014521.2		2642,2591,1270	GG,GA,AA		46.4419,11.9156,39.451		802/964	235951819	7875,5131	2203	4300	6503	SO:0001819	synonymous_variant	23677	exon4			CGTCCTAGAAAAG	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.2406A>G	2.37:g.235951819A>G		Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	176	10	0.0568182	NM_014521	O95082|Q309A3|Q53QD0|Q53TD1	Silent	SNP	ENST00000409212.1	37	CCDS2513.1																																																																																			G|0.647;N|0.001	0.647	strong		0.587	SH3BP4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329763.1		
CDC27	996	hgsc.bcm.edu	37	17	45234327	45234327	+	Missense_Mutation	SNP	C	C	T	rs7350889		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr17:45234327C>T	ENST00000066544.3	-	7	887	c.794G>A	c.(793-795)gGt>gAt	p.G265D	CDC27_ENST00000527547.1_Missense_Mutation_p.G265D|CDC27_ENST00000528748.1_5'Flank|CDC27_ENST00000446365.2_Missense_Mutation_p.G204D|CDC27_ENST00000531206.1_Missense_Mutation_p.G265D	NM_001114091.1|NM_001256.3	NP_001107563.1|NP_001247.3	P30260	CDC27_HUMAN	cell division cycle 27	265					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cell cycle (GO:0000278)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	protein phosphatase binding (GO:0019903)	p.G265D(2)		NS(1)|breast(5)|central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(17)|large_intestine(18)|lung(11)|ovary(5)|pancreas(1)|prostate(19)|skin(5)|upper_aerodigestive_tract(2)	90						TAAACTTCGACCAGTTTTTGG	0.368																																					p.G265D		Atlas-SNP	.											CDC27_ENST00000531206,NS,adenoma,0,4	CDC27	337	4	2	Substitution - Missense(2)	skin(2)	c.G794A						scavenged	.						60.0	65.0	63.0					17																	45234327		2201	4295	6496	SO:0001583	missense	996	exon7			CTTCGACCAGTTT	U00001	CCDS11509.1, CCDS45720.1, CCDS74090.1	17q21.32	2013-01-17	2013-01-17		ENSG00000004897	ENSG00000004897		"""Anaphase promoting complex subunits"", ""Tetratricopeptide (TTC) repeat domain containing"""	1728	protein-coding gene	gene with protein product	"""anaphase promoting complex subunit 3"""	116946	"""cell division cycle 27"", ""cell division cycle 27 homolog (S. cerevisiae)"""	D0S1430E, D17S978E		8234252	Standard	XM_005257892		Approved	APC3, ANAPC3, NUC2	uc002ile.4	P30260	OTTHUMG00000166429	ENST00000066544.3:c.794G>A	17.37:g.45234327C>T	ENSP00000066544:p.Gly265Asp	Somatic	73	1	0.0136986		WXS	Illumina HiSeq	Phase_I	78	5	0.0641026	NM_001114091	G3V1C4|Q16349|Q96F35	Missense_Mutation	SNP	ENST00000066544.3	37	CCDS11509.1	.	.	.	.	.	.	.	.	.	.	C	15.07	2.725453	0.48833	.	.	ENSG00000004897	ENST00000066544;ENST00000531206;ENST00000446365;ENST00000527547;ENST00000526866	T;T;T;T;T	0.68181	-0.31;-0.3;-0.11;-0.31;0.86	5.64	5.64	0.86602	.	0.000000	0.85682	D	0.000000	T	0.52853	0.1760	N	0.24115	0.695	0.80722	D	1	B;B;B;B	0.32350	0.251;0.366;0.247;0.251	B;B;B;B	0.27076	0.045;0.056;0.076;0.055	T	0.51694	-0.8673	10	0.33141	T	0.24	1.6987	17.2083	0.86924	0.0:1.0:0.0:0.0	rs7350889;rs7350889	204;265;265;265	B4DL80;G5EA36;G3V1C4;P30260	.;.;.;CDC27_HUMAN	D	265;265;204;265;265	ENSP00000066544:G265D;ENSP00000434614:G265D;ENSP00000392802:G204D;ENSP00000437339:G265D;ENSP00000432105:G265D	ENSP00000066544:G265D	G	-	2	0	CDC27	42589326	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.618000	0.67722	2.665000	0.90641	0.460000	0.39030	GGT	C|1.000;|0.000	.	weak		0.368	CDC27-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389742.2		
TTN	7273	hgsc.bcm.edu	37	2	179604859	179604859	+	Missense_Mutation	SNP	C	C	A	rs367656813		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr2:179604859C>A	ENST00000591111.1	-	46	12374	c.12150G>T	c.(12148-12150)aaG>aaT	p.K4050N	TTN-AS1_ENST00000582847.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.K4004N|TTN_ENST00000589042.1_Missense_Mutation_p.K4367N|TTN-AS1_ENST00000590773.1_RNA|TTN_ENST00000342992.6_Intron|TTN_ENST00000359218.5_Missense_Mutation_p.K4129N|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.K4196N			Q8WZ42	TITIN_HUMAN	titin	0					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)			CCTGCACTTTCTTTATTGCCA	0.443																																					p.K4367N		Atlas-SNP	.											.	TTN	18412	.	0			c.G13101T						PASS	.	C	ASN/LYS,,ASN/LYS,ASN/LYS	1,3693		0,1,1846	67.0	66.0	66.0		12012,,12387,12588	-3.0	0.0	2		66	0,8188		0,0,4094	no	missense,intron,missense,missense	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	94,,94,94	0,1,5940	AA,AC,CC		0.0,0.0271,0.0084	,,,	4004/26927,,4129/27052,4196/27119	179604859	1,11881	1847	4094	5941	SO:0001583	missense	7273	exon48			CACTTTCTTTATT	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.12150G>T	2.37:g.179604859C>A	ENSP00000465570:p.Lys4050Asn	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	109	29	0.266055	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		.	.	.	.	.	.	.	.	.	.	C	1.754	-0.488428	0.04352	2.71E-4	0.0	ENSG00000155657	ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T	0.61859	0.14;0.08;0.07	5.92	-3.05	0.05396	.	.	.	.	.	T	0.29190	0.0726	N	0.08118	0	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	0.12116	-1.0560	9	0.87932	D	0	.	1.5845	0.02641	0.2937:0.3519:0.1844:0.17	.	4004;4129;4196	D3DPF9;E7EQE6;E7ET18	.;.;.	N	4004;4196;4129;4004	ENSP00000434586:K4004N;ENSP00000340554:K4196N;ENSP00000352154:K4129N	ENSP00000340554:K4196N	K	-	3	2	TTN	179313104	0.001000	0.12720	0.000000	0.03702	0.000000	0.00434	0.294000	0.19047	-1.056000	0.03205	-0.182000	0.12963	AAG	.	.	weak		0.443	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
PRAMEF11	440560	hgsc.bcm.edu	37	1	12887686	12887686	+	Silent	SNP	T	T	C	rs59802947	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr1:12887686T>C	ENST00000535591.1	-	3	366	c.171A>G	c.(169-171)agA>agG	p.R57R		NM_001146344.1	NP_001139816.1	O60813	PRA11_HUMAN	PRAME family member 11	57					negative regulation of apoptotic process (GO:0043066)|negative regulation of cell differentiation (GO:0045596)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)			p.R57R(1)		NS(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|lung(7)|pancreas(2)|skin(4)|urinary_tract(1)	27						GAAGTTTCCATCTCCTGTGGG	0.468													.|||	5	0.000998403	0.0008	0.0	5008	,	,		21622	0.001		0.0	False		,,,				2504	0.0031				p.R57R		Atlas-SNP	.											PRAMEF11,NS,carcinoma,0,1	PRAMEF11	72	1	1	Substitution - coding silent(1)	endometrium(1)	c.A171G						scavenged	.																																			SO:0001819	synonymous_variant	440560	exon3			TTTCCATCTCCTG	AL049680	CCDS53268.1	1p36.21	2013-01-17			ENSG00000204513	ENSG00000239810		"""-"""	14086	protein-coding gene	gene with protein product							Standard	XM_006710645		Approved		uc001auk.2	O60813	OTTHUMG00000001929	ENST00000535591.1:c.171A>G	1.37:g.12887686T>C		Somatic	9	0	0		WXS	Illumina HiSeq	Phase_I	16	4	0.25	NM_001146344		Silent	SNP	ENST00000535591.1	37	CCDS53268.1																																																																																			T|0.986;C|0.014	0.014	strong		0.468	PRAMEF11-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		XM_496341	
CNTN6	27255	hgsc.bcm.edu	37	3	1414127	1414127	+	Missense_Mutation	SNP	A	A	G	rs145045076	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr3:1414127A>G	ENST00000446702.2	+	13	2264	c.1637A>G	c.(1636-1638)aAa>aGa	p.K546R	CNTN6_ENST00000539053.1_Missense_Mutation_p.K474R|CNTN6_ENST00000350110.2_Missense_Mutation_p.K546R			Q9UQ52	CNTN6_HUMAN	contactin 6	546	Ig-like C2-type 6.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|central nervous system development (GO:0007417)|Notch signaling pathway (GO:0007219)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				breast(6)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(25)|lung(34)|ovary(1)|pancreas(1)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	90		all_cancers(2;0.000164)|all_epithelial(2;0.107)		Epithelial(13;0.000233)|all cancers(10;0.0013)|OV - Ovarian serous cystadenocarcinoma(96;0.0139)		GACTTAAAAAAAGGAGTGGCT	0.373													A|||	17	0.00339457	0.0	0.0	5008	,	,		16370	0.0169		0.0	False		,,,				2504	0.0				p.K546R		Atlas-SNP	.											CNTN6,NS,lymphoid_neoplasm,0,1	CNTN6	245	1	0			c.A1637G						PASS	.						107.0	108.0	107.0					3																	1414127		2203	4300	6503	SO:0001583	missense	27255	exon13			TAAAAAAAGGAGT	AB003592	CCDS2557.1	3p26-p25	2013-02-11			ENSG00000134115	ENSG00000134115		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	2176	protein-coding gene	gene with protein product	"""neural adhesion molecule"""	607220				9486763	Standard	NM_014461		Approved	NB-3	uc003bpa.3	Q9UQ52	OTTHUMG00000119030	ENST00000446702.2:c.1637A>G	3.37:g.1414127A>G	ENSP00000407822:p.Lys546Arg	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	93	4	0.0430108	NM_014461	Q2KHM2	Missense_Mutation	SNP	ENST00000446702.2	37	CCDS2557.1	13	0.005952380952380952	0	0.0	0	0.0	13	0.022727272727272728	0	0.0	A	13.60	2.286128	0.40394	.	.	ENSG00000134115	ENST00000446702;ENST00000539053;ENST00000350110	T;T;T	0.67345	-0.26;-0.26;-0.26	5.8	4.67	0.58626	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.327961	0.27245	N	0.020260	T	0.25121	0.0610	N	0.12471	0.22	0.27294	N	0.95778	B	0.13145	0.007	B	0.12156	0.007	T	0.04752	-1.0929	10	0.25106	T	0.35	.	3.1712	0.06552	0.635:0.0:0.1551:0.2099	.	546	Q9UQ52	CNTN6_HUMAN	R	546;474;546	ENSP00000407822:K546R;ENSP00000442791:K474R;ENSP00000341882:K546R	ENSP00000341882:K546R	K	+	2	0	CNTN6	1389127	1.000000	0.71417	0.998000	0.56505	0.964000	0.63967	4.410000	0.59774	2.206000	0.71126	0.528000	0.53228	AAA	A|0.994;G|0.006	0.006	strong		0.373	CNTN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239235.2	NM_014461	
KIAA0196	9897	hgsc.bcm.edu	37	8	126069044	126069044	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr8:126069044G>A	ENST00000318410.7	-	16	2240	c.1891C>T	c.(1891-1893)Cca>Tca	p.P631S	KIAA0196_ENST00000517845.1_Missense_Mutation_p.P483S	NM_014846.3	NP_055661.3	Q12768	STRUM_HUMAN	KIAA0196	631					cell death (GO:0008219)|endosomal transport (GO:0016197)	endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|WASH complex (GO:0071203)				NS(1)|breast(3)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(7)|lung(15)|ovary(2)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(2)	42	Ovarian(258;0.0028)|all_neural(195;0.00294)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.000918)|COAD - Colon adenocarcinoma(160;0.205)			ATGCTTTCTGGGATGATCTGC	0.408																																					p.P631S		Atlas-SNP	.											KIAA0196,NS,malignant_melanoma,0,1	KIAA0196	90	1	0			c.C1891T						PASS	.						156.0	146.0	149.0					8																	126069044		2203	4300	6503	SO:0001583	missense	9897	exon16			TTTCTGGGATGAT		CCDS6355.1	8q24.13	2014-05-09			ENSG00000164961	ENSG00000164961			28984	protein-coding gene	gene with protein product	"""strumpellin"""	610657	"""spastic paraplegia 8 (autosomal dominant)"""	SPG8		9973294, 17160902, 23085491	Standard	NM_014846		Approved		uc003yrt.3	Q12768	OTTHUMG00000164991	ENST00000318410.7:c.1891C>T	8.37:g.126069044G>A	ENSP00000318016:p.Pro631Ser	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	73	23	0.315068	NM_014846	A8K4R7|Q3KQX5|Q8TBQ2	Missense_Mutation	SNP	ENST00000318410.7	37	CCDS6355.1	.	.	.	.	.	.	.	.	.	.	G	28.7	4.944848	0.92593	.	.	ENSG00000164961	ENST00000318410;ENST00000517845	D;D	0.96300	-3.97;-3.97	5.35	5.35	0.76521	.	0.000000	0.85682	D	0.000000	D	0.98457	0.9486	M	0.88310	2.945	0.80722	D	1	D;D	0.89917	1.0;0.997	D;D	0.97110	1.0;0.995	D	0.99289	1.0898	10	0.87932	D	0	-11.8017	19.4322	0.94775	0.0:0.0:1.0:0.0	.	483;631	E7EQI7;Q12768	.;STRUM_HUMAN	S	631;483	ENSP00000318016:P631S;ENSP00000429676:P483S	ENSP00000318016:P631S	P	-	1	0	KIAA0196	126138226	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	9.809000	0.99208	2.649000	0.89929	0.655000	0.94253	CCA	.	.	none		0.408	KIAA0196-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381369.1	NM_014846	
KIF20B	9585	hgsc.bcm.edu	37	10	91470834	91470834	+	Silent	SNP	A	A	C	rs1048057	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr10:91470834A>C	ENST00000371728.3	+	6	672	c.607A>C	c.(607-609)Agg>Cgg	p.R203R	KIF20B_ENST00000416354.1_Silent_p.R203R|KIF20B_ENST00000394289.2_Silent_p.R203R|KIF20B_ENST00000260753.4_Silent_p.R203R	NM_001284259.1	NP_001271188.1	Q96Q89	KI20B_HUMAN	kinesin family member 20B	203	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|cell cycle arrest (GO:0007050)|microtubule-based movement (GO:0007018)|mitotic nuclear division (GO:0007067)|neural tube closure (GO:0001843)|regulation of establishment of cell polarity (GO:2000114)|regulation of establishment of protein localization (GO:0070201)|regulation of mitosis (GO:0007088)|regulation of neuron migration (GO:2001222)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|WW domain binding (GO:0050699)	p.R203R(1)		endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(20)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)	58						AGAATACTTAAGGTTATCATC	0.323													C|||	2321	0.463458	0.5749	0.3847	5008	,	,		20058	0.5665		0.2396	False		,,,				2504	0.4928				p.R203R		Atlas-SNP	.											KIF20B,NS,carcinoma,0,1	KIF20B	191	1	1	Substitution - coding silent(1)	stomach(1)	c.A607C						scavenged	.	C		2405,2001	551.7+/-378.3	654,1097,452	67.0	72.0	70.0		607	3.5	1.0	10	dbSNP_86	70	2076,6522	715.3+/-406.0	237,1602,2460	no	coding-synonymous	KIF20B	NM_016195.2		891,2699,2912	CC,CA,AA		24.1452,45.4153,34.4586		203/1781	91470834	4481,8523	2203	4299	6502	SO:0001819	synonymous_variant	9585	exon6			TACTTAAGGTTAT	L16782	CCDS7407.1, CCDS60590.1	10q23.31	2009-08-06	2008-07-31	2008-07-31	ENSG00000138182	ENSG00000138182			7212	protein-coding gene	gene with protein product	"""cancer/testis antigen 90"""	605498	"""M-phase phosphoprotein 1"""	MPHOSPH1		8885239, 8290587, 11470801	Standard	NM_016195		Approved	MPP1, KRMP1, CT90	uc001kgr.1	Q96Q89	OTTHUMG00000018725	ENST00000371728.3:c.607A>C	10.37:g.91470834A>C		Somatic	247	0	0		WXS	Illumina HiSeq	Phase_I	205	6	0.0292683	NM_016195	A8MXM7|O43277|Q09471|Q2KQ73|Q32NE1|Q561V3|Q58EX8|Q5T9M8|Q5T9M9|Q5T9N0|Q5T9N1|Q7KZ68|Q7Z5E0|Q7Z5E1|Q7Z6M9|Q86X82|Q9H3R8|Q9H6Q9|Q9H755|Q9NTC1|Q9UFR5	Silent	SNP	ENST00000371728.3	37																																																																																				A|0.632;C|0.368	0.368	strong		0.323	KIF20B-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000049330.1	NM_016195	
SAMD9L	219285	hgsc.bcm.edu	37	7	92762681	92762681	+	Silent	SNP	A	A	G	rs1029357	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr7:92762681A>G	ENST00000318238.4	-	5	3820	c.2604T>C	c.(2602-2604)gcT>gcC	p.A868A	SAMD9L_ENST00000411955.1_Silent_p.A868A|SAMD9L_ENST00000437805.1_Silent_p.A868A	NM_152703.2	NP_689916.2	Q8IVG5	SAM9L_HUMAN	sterile alpha motif domain containing 9-like	868					common myeloid progenitor cell proliferation (GO:0035726)|endosomal vesicle fusion (GO:0034058)|hematopoietic progenitor cell differentiation (GO:0002244)|regulation of protein catabolic process (GO:0042176)|spleen development (GO:0048536)|stem cell division (GO:0017145)	early endosome (GO:0005769)		p.A868A(1)		central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(23)|liver(2)|lung(31)|ovary(5)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	88	all_cancers(62;4.15e-11)|all_epithelial(64;2.29e-10)|Breast(17;0.000675)|Lung NSC(181;0.0755)|all_lung(186;0.0989)		STAD - Stomach adenocarcinoma(171;0.000302)			TGGCACCAAAAGCTCTTTGTT	0.353													A|||	1456	0.290735	0.5174	0.3285	5008	,	,		21598	0.3482		0.0716	False		,,,				2504	0.1237				p.A868A		Atlas-SNP	.											SAMD9L,NS,carcinoma,0,1	SAMD9L	227	1	1	Substitution - coding silent(1)	stomach(1)	c.T2604C						scavenged	.	A		1856,2548	517.3+/-369.4	407,1042,753	83.0	92.0	89.0		2604	-0.6	1.0	7	dbSNP_86	89	705,7893	172.3+/-223.0	29,647,3623	no	coding-synonymous	SAMD9L	NM_152703.2		436,1689,4376	GG,GA,AA		8.1996,42.1435,19.697		868/1585	92762681	2561,10441	2202	4299	6501	SO:0001819	synonymous_variant	219285	exon5			ACCAAAAGCTCTT	AB095926	CCDS34681.1	7q21.2	2013-01-10		2005-04-26	ENSG00000177409	ENSG00000177409		"""Sterile alpha motif (SAM) domain containing"""	1349	protein-coding gene	gene with protein product		611170	"""chromosome 7 open reading frame 6"""	C7orf6			Standard	NM_152703		Approved	KIAA2005, FLJ39885	uc003umh.1	Q8IVG5	OTTHUMG00000155807	ENST00000318238.4:c.2604T>C	7.37:g.92762681A>G		Somatic	131	1	0.00763359		WXS	Illumina HiSeq	Phase_I	114	4	0.0350877	NM_152703	A0JP23|A0JP24|A0PJG8|A4D1G8|D6W5Q6|Q2TV71|Q2TV75|Q2UZV8|Q8IWI4|Q8N3L9|Q8N875	Silent	SNP	ENST00000318238.4	37	CCDS34681.1																																																																																			A|0.774;G|0.226	0.226	strong		0.353	SAMD9L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341730.1	NM_152703	
PRDM15	63977	hgsc.bcm.edu	37	21	43221555	43221555	+	Silent	SNP	G	G	A	rs2236694	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr21:43221555G>A	ENST00000269844.3	-	31	4479	c.4369C>T	c.(4369-4371)Ctg>Ttg	p.L1457L	PRDM15_ENST00000422911.1_Silent_p.L1148L|PRDM15_ENST00000470586.1_5'UTR|PRDM15_ENST00000398548.1_Silent_p.L1128L|PRDM15_ENST00000447207.2_Silent_p.L1091L|PRDM15_ENST00000538201.1_Silent_p.L1111L	NM_022115.3	NP_071398.3	P57071	PRD15_HUMAN	PR domain containing 15	1457					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)	p.L1457L(1)		NS(2)|breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(11)|ovary(3)|skin(2)|stomach(2)|urinary_tract(1)	43						TGGCTCCCCAGGGGCGTGATG	0.647													g|||	499	0.0996406	0.0265	0.062	5008	,	,		16209	0.1558		0.1054	False		,,,				2504	0.1616				p.L1457L		Atlas-SNP	.											PRDM15,NS,carcinoma,0,1	PRDM15	110	1	1	Substitution - coding silent(1)	stomach(1)	c.C4369T						scavenged	.		,	156,4250	106.5+/-144.9	3,150,2050	84.0	74.0	78.0		3382,4369	2.5	1.0	21	dbSNP_98	78	808,7792	188.9+/-235.7	38,732,3530	no	coding-synonymous,coding-synonymous	PRDM15	NM_001040424.1,NM_022115.3	,	41,882,5580	AA,AG,GG		9.3953,3.5406,7.412	,	1128/1179,1457/1508	43221555	964,12042	2203	4300	6503	SO:0001819	synonymous_variant	63977	exon31			TCCCCAGGGGCGT	AF276513	CCDS13676.1, CCDS42932.1, CCDS63370.1	21q22.3	2013-01-08	2002-07-31		ENSG00000141956	ENSG00000141956		"""Zinc fingers, C2H2-type"""	13999	protein-coding gene	gene with protein product			"""chromosome 21 open reading frame 83"""	ZNF298, C21orf83		12036297, 12036298	Standard	NM_022115		Approved		uc002yzq.1	P57071	OTTHUMG00000086781	ENST00000269844.3:c.4369C>T	21.37:g.43221555G>A		Somatic	106	1	0.00943396		WXS	Illumina HiSeq	Phase_I	121	8	0.0661157	NM_022115	E9PDJ6|E9PF37|E9PGL3|Q4W8S0|Q4W8S3|Q4W8S4|Q4W8S5|Q8N0X3|Q8NEX0|Q9NQV3	Silent	SNP	ENST00000269844.3	37	CCDS13676.1																																																																																			G|0.915;A|0.085	0.085	strong		0.647	PRDM15-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_022115	
ANKRD11	29123	hgsc.bcm.edu	37	16	89348038	89348038	+	Missense_Mutation	SNP	G	G	C	rs113527563	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr16:89348038G>C	ENST00000301030.4	-	9	5372	c.4912C>G	c.(4912-4914)Cct>Gct	p.P1638A	ANKRD11_ENST00000378330.2_Missense_Mutation_p.P1638A	NM_001256183.1|NM_013275.5	NP_001243112.1|NP_037407.4	Q6UB99	ANR11_HUMAN	ankyrin repeat domain 11	1638	Lys-rich.				bone development (GO:0060348)|face morphogenesis (GO:0060325)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|odontogenesis of dentin-containing tooth (GO:0042475)|skeletal system morphogenesis (GO:0048705)|tissue homeostasis (GO:0001894)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.P1638A(1)		breast(4)|central_nervous_system(3)|endometrium(17)|kidney(2)|large_intestine(18)|lung(20)|ovary(6)|pancreas(1)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	83		all_hematologic(23;0.00824)|Colorectal(91;0.0475)		Epithelial(1;5.33e-11)|all cancers(4;2.6e-09)|OV - Ovarian serous cystadenocarcinoma(4;2.29e-07)|BRCA - Breast invasive adenocarcinoma(80;0.0142)		TTCTTAGCAGGAATGTCCAGA	0.562													G|||	527	0.105232	0.034	0.0807	5008	,	,		13862	0.245		0.0129	False		,,,				2504	0.1697				p.P1638A		Atlas-SNP	.											ANKRD11,NS,carcinoma,0,1	ANKRD11	195	1	1	Substitution - Missense(1)	stomach(1)	c.C4912G						scavenged	.	G	ALA/PRO	128,4268	89.2+/-127.9	3,122,2073	95.0	106.0	102.0		4912	1.9	0.0	16	dbSNP_132	102	36,8564	22.2+/-67.0	0,36,4264	yes	missense	ANKRD11	NM_013275.4	27	3,158,6337	CC,CG,GG		0.4186,2.9117,1.2619	possibly-damaging	1638/2664	89348038	164,12832	2198	4300	6498	SO:0001583	missense	29123	exon9			TAGCAGGAATGTC	AY373756	CCDS32513.1	16q24.3	2013-01-10				ENSG00000167522		"""Ankyrin repeat domain containing"""	21316	protein-coding gene	gene with protein product		611192				11483580	Standard	NM_001256182		Approved	LZ16, T13	uc002fnc.2	Q6UB99		ENST00000301030.4:c.4912C>G	16.37:g.89348038G>C	ENSP00000301030:p.Pro1638Ala	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	75	2	0.0266667	NM_001256183	Q6NTG1|Q6QMF8	Missense_Mutation	SNP	ENST00000301030.4	37	CCDS32513.1	176	0.08058608058608059	23	0.046747967479674794	18	0.049723756906077346	122	0.21328671328671328	13	0.017150395778364115	G	5.052	0.195221	0.09599	0.029117	0.004186	ENSG00000167522	ENST00000301030;ENST00000378330	T;T	0.35789	1.29;1.29	5.07	1.89	0.25635	.	0.256644	0.32901	N	0.005511	T	0.00012	0.0000	L	0.29908	0.895	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.24476	-1.0159	9	0.28530	T	0.3	.	3.4272	0.07414	0.079:0.2782:0.3568:0.286	.	1638	Q6UB99	ANR11_HUMAN	A	1638	ENSP00000301030:P1638A;ENSP00000367581:P1638A	ENSP00000301030:P1638A	P	-	1	0	ANKRD11	87875539	0.612000	0.27000	0.002000	0.10522	0.001000	0.01503	0.943000	0.29030	0.140000	0.18849	-0.502000	0.04539	CCT	G|0.966;C|0.034	0.034	strong		0.562	ANKRD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430462.3	NM_013275	
NDUFB1	4707	hgsc.bcm.edu	37	14	92588002	92588002	+	5'UTR	SNP	T	T	G	rs3818263	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr14:92588002T>G	ENST00000553514.1	-	0	66				NDUFB1_ENST00000556555.1_5'UTR|NDUFB1_ENST00000555441.1_5'Flank|NDUFB1_ENST00000329559.3_Silent_p.V40V|CPSF2_ENST00000298875.4_5'Flank|NDUFB1_ENST00000605997.1_5'UTR			O75438	NDUB1_HUMAN	NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 1, 7kDa						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)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			large_intestine(1)|lung(1)	2		all_cancers(154;0.0766)		COAD - Colon adenocarcinoma(157;0.205)		CCTCAGCGCCTACAGCGACCC	0.711													G|||	2703	0.539736	0.5514	0.379	5008	,	,		10980	0.8552		0.334	False		,,,				2504	0.5245				p.V40V		Atlas-SNP	.											NDUFB1,rectum,carcinoma,0,1	NDUFB1	5	1	0			c.A120C						scavenged	.	G		2232,2174		573,1086,544	33.0	39.0	37.0		120	-7.0	0.0	14	dbSNP_107	37	2915,5681		489,1937,1872	no	coding-synonymous	NDUFB1	NM_004545.3		1062,3023,2416	GG,GT,TT		33.9111,49.3418,39.5862		40/106	92588002	5147,7855	2203	4298	6501	SO:0001623	5_prime_UTR_variant	4707	exon1			AGCGCCTACAGCG	BC104672	CCDS9901.1	14q31.3	2011-07-04	2002-08-29		ENSG00000183648	ENSG00000183648		"""Mitochondrial respiratory chain complex / Complex I"""	7695	protein-coding gene	gene with protein product	"""complex I MNLL subunit"""	603837	"""NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 1 (7kD, MNLL)"""			9763677	Standard	NM_004545		Approved	MNLL, CI-MNLL	uc001yaf.3	O75438		ENST00000553514.1:c.-140A>C	14.37:g.92588002T>G		Somatic	148	1	0.00675676		WXS	Illumina HiSeq	Phase_I	170	6	0.0352941	NM_004545	A0AV68	Silent	SNP	ENST00000553514.1	37																																																																																				T|0.520;G|0.480	0.480	strong		0.711	NDUFB1-004	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000412116.2	NM_004545	
LRRC3B	116135	hgsc.bcm.edu	37	3	26751493	26751493	+	Silent	SNP	A	A	T	rs35497952	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr3:26751493A>T	ENST00000396641.2	+	2	922	c.330A>T	c.(328-330)ggA>ggT	p.G110G	LRRC3B_ENST00000456208.2_Silent_p.G110G|LRRC3B_ENST00000417744.1_Silent_p.G110G|AC114877.3_ENST00000446601.1_lincRNA	NM_052953.2	NP_443185.1	Q96PB8	LRC3B_HUMAN	leucine rich repeat containing 3B	110						integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(4)|ovary(1)|pancreas(2)|prostate(1)|skin(4)	21						CCTTCAAAGGAGTAGCTGAAA	0.438													A|||	739	0.147564	0.1036	0.1556	5008	,	,		21624	0.2421		0.0805	False		,,,				2504	0.1728				p.G110G		Atlas-SNP	.											.	LRRC3B	51	.	0			c.A330T						PASS	.	A		439,3967	212.5+/-232.4	20,399,1784	65.0	62.0	63.0		330	-4.1	0.9	3	dbSNP_126	63	764,7836	181.8+/-230.4	43,678,3579	no	coding-synonymous	LRRC3B	NM_052953.2		63,1077,5363	TT,TA,AA		8.8837,9.9637,9.2496		110/260	26751493	1203,11803	2203	4300	6503	SO:0001819	synonymous_variant	116135	exon2			CAAAGGAGTAGCT	AF396933	CCDS2644.1	3p24	2004-07-12			ENSG00000179796	ENSG00000179796			28105	protein-coding gene	gene with protein product							Standard	NM_052953		Approved	LRP15	uc003cdp.3	Q96PB8	OTTHUMG00000130572	ENST00000396641.2:c.330A>T	3.37:g.26751493A>T		Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	116	8	0.0689655	NM_052953	Q5M8T0	Silent	SNP	ENST00000396641.2	37	CCDS2644.1																																																																																			A|0.898;T|0.102	0.102	strong		0.438	LRRC3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252997.2	NM_052953	
NRAP	4892	hgsc.bcm.edu	37	10	115410234	115410234	+	Missense_Mutation	SNP	T	T	C	rs2185913	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr10:115410234T>C	ENST00000359988.3	-	8	990	c.746A>G	c.(745-747)tAt>tGt	p.Y249C	NRAP_ENST00000369360.3_Missense_Mutation_p.Y249C|NRAP_ENST00000360478.3_Missense_Mutation_p.Y249C|NRAP_ENST00000369358.4_Missense_Mutation_p.Y249C	NM_001261463.1|NM_198060.3	NP_001248392.1|NP_932326.2			nebulin-related anchoring protein									p.Y249C(1)		autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(18)|lung(39)|ovary(6)|prostate(3)|skin(1)|stomach(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	95		Colorectal(252;0.0233)|Breast(234;0.188)		Epithelial(162;0.00392)|all cancers(201;0.00569)		GGCTATCTGATAGGCGGGTGT	0.458													T|||	1019	0.203474	0.0182	0.245	5008	,	,		22449	0.3343		0.3012	False		,,,				2504	0.1892				p.Y249C		Atlas-SNP	.											NRAP,NS,carcinoma,0,1	NRAP	208	1	1	Substitution - Missense(1)	stomach(1)	c.A746G						scavenged	.	T	CYS/TYR,CYS/TYR	256,4150	148.0+/-182.4	12,232,1959	193.0	156.0	169.0		746,746	6.2	1.0	10	dbSNP_96	169	2512,6088	411.5+/-350.5	351,1810,2139	yes	missense,missense	NRAP	NM_006175.3,NM_198060.2	194,194	363,2042,4098	CC,CT,TT		29.2093,5.8103,21.2825	probably-damaging,probably-damaging	249/1696,249/1731	115410234	2768,10238	2203	4300	6503	SO:0001583	missense	4892	exon8			ATCTGATAGGCGG		CCDS7578.1, CCDS7579.1, CCDS73199.1	10q24-q26	2008-08-01			ENSG00000197893	ENSG00000197893			7988	protein-coding gene	gene with protein product		602873				12789664, 10320340	Standard	NM_006175		Approved		uc001lal.4	Q86VF7	OTTHUMG00000019072	ENST00000359988.3:c.746A>G	10.37:g.115410234T>C	ENSP00000353078:p.Tyr249Cys	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	129	5	0.0387597	NM_001261463		Missense_Mutation	SNP	ENST00000359988.3	37	CCDS7579.1	531	0.24313186813186813	14	0.028455284552845527	100	0.27624309392265195	199	0.3479020979020979	218	0.287598944591029	T	24.3	4.512888	0.85389	0.058103	0.292093	ENSG00000197893	ENST00000369358;ENST00000369360;ENST00000359988;ENST00000360478	T;T;T;T	0.20463	2.32;2.25;2.18;2.07	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	M	0.79123	2.44	0.18873	P	0.9999877178	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.998	T	0.10683	-1.0619	9	0.66056	D	0.02	.	16.8222	0.85835	0.0:0.0:0.0:1.0	rs2185913;rs17773512;rs59388325;rs2185913	249;249	Q86VF7-4;Q86VF7	.;NRAP_HUMAN	C	249	ENSP00000358365:Y249C;ENSP00000358367:Y249C;ENSP00000353078:Y249C;ENSP00000353666:Y249C	ENSP00000353078:Y249C	Y	-	2	0	NRAP	115400224	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.283000	0.78640	2.371000	0.80710	0.533000	0.62120	TAT	T|0.781;C|0.219	0.219	strong		0.458	NRAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050425.2	NM_006175	
SIRPB1	10326	hgsc.bcm.edu	37	20	1592193	1592193	+	Intron	SNP	C	C	T	rs371465078	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr20:1592193C>T	ENST00000381605.4	-	1	141				SIRPB1_ENST00000381603.3_Intron|SIRPB1_ENST00000568365.1_Silent_p.Q81Q|SIRPB1_ENST00000279477.7_Silent_p.Q81Q|SIRPB1_ENST00000381596.1_5'UTR|RP4-576H24.4_ENST00000564763.1_Intron	NM_006065.3	NP_006056.2	O00241	SIRB1_HUMAN	signal-regulatory protein beta 1						cell surface receptor signaling pathway (GO:0007166)|innate immune response (GO:0045087)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				central_nervous_system(2)|kidney(2)|large_intestine(4)|lung(16)|ovary(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)	31						GGCCTTCTTTCTGATTGTAGA	0.522													t|||	2823	0.563698	0.68	0.3876	5008	,	,		6072	0.631		0.3748	False		,,,				2504	0.6564				p.Q81Q		Atlas-SNP	.											SIRPB1_ENST00000279477,NS,malignant_melanoma,0,1	SIRPB1	83	1	0			c.G243A						scavenged	.						94.0	111.0	106.0					20																	1592193		447	1317	1764	SO:0001627	intron_variant	10326	exon2			TTCTTTCTGATTG	Y10376	CCDS13019.1, CCDS42850.1, CCDS46571.1	20p13	2013-01-11			ENSG00000101307	ENSG00000101307		"""Signal-regulatory proteins"", ""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C1-set domain containing"""	15928	protein-coding gene	gene with protein product		603889				9062191, 16339511	Standard	NM_001083910		Approved	SIRP-BETA-1, CD172b	uc010gai.3	O00241	OTTHUMG00000031676	ENST00000381605.4:c.76+8321G>A	20.37:g.1592193C>T		Somatic	138	6	0.0434783		WXS	Illumina HiSeq	Phase_I	141	7	0.0496454	NM_001135844	A6NLM2|B2R8V0|Q5TFQ9|Q5TFR0|Q8TB12|Q9H1U5|Q9Y4V0	Silent	SNP	ENST00000381605.4	37	CCDS13019.1																																																																																			.	.	weak		0.522	SIRPB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077555.2	NM_006065	
PRAMEF10	343071	hgsc.bcm.edu	37	1	12954852	12954852	+	Missense_Mutation	SNP	T	T	C	rs200815222	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr1:12954852T>C	ENST00000235347.4	-	3	510	c.431A>G	c.(430-432)cAc>cGc	p.H144R		NM_001039361.3	NP_001034450.2	O60809	PRA10_HUMAN	PRAME family member 10	144			H -> R (in dbSNP:rs2797709).		negative regulation of apoptotic process (GO:0043066)|negative regulation of cell differentiation (GO:0045596)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)			p.H144R(1)		NS(2)|breast(1)|large_intestine(2)|lung(5)|ovary(1)|upper_aerodigestive_tract(1)	12	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.00224)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;4.88e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|COAD - Colon adenocarcinoma(227;0.000241)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		CAAGGGCTGGTGCTCTCCCAT	0.527													N|||	85	0.0169728	0.0197	0.0331	5008	,	,		14277	0.0089		0.0089	False		,,,				2504	0.0184				p.H144R		Atlas-SNP	.											PRAMEF10,NS,NS,0,1	PRAMEF10	35	1	1	Substitution - Missense(1)	NS(1)	c.A431G						scavenged	.						126.0	129.0	128.0					1																	12954852		1982	3990	5972	SO:0001583	missense	343071	exon3			GGCTGGTGCTCTC	AL049682	CCDS41255.1	1p36.21	2013-01-17			ENSG00000187545	ENSG00000187545		"""-"""	27997	protein-coding gene	gene with protein product							Standard	NM_001039361		Approved		uc001auo.3	O60809	OTTHUMG00000001981	ENST00000235347.4:c.431A>G	1.37:g.12954852T>C	ENSP00000235347:p.His144Arg	Somatic	29	4	0.137931		WXS	Illumina HiSeq	Phase_I	27	6	0.222222	NM_001039361	Q2M1V2	Missense_Mutation	SNP	ENST00000235347.4	37	CCDS41255.1	.	.	.	.	.	.	.	.	.	.	.	0.008	-1.869932	0.00542	.	.	ENSG00000187545	ENST00000235347	T	0.14766	2.48	1.65	-3.3	0.05003	.	2.458840	0.02019	N	0.047646	T	0.04318	0.0119	N	0.02266	-0.62	0.80722	P	0.0	B	0.02656	0.0	B	0.09377	0.004	T	0.31530	-0.9940	9	0.02654	T	1	.	4.9328	0.13926	0.0:0.4645:0.2179:0.3176	.	144	O60809	PRA10_HUMAN	R	144	ENSP00000235347:H144R	ENSP00000235347:H144R	H	-	2	0	PRAMEF10	12877439	0.000000	0.05858	0.000000	0.03702	0.019000	0.09904	-1.840000	0.01684	-1.846000	0.01175	-2.717000	0.00132	CAC	T|0.500;C|0.500	0.500	weak		0.527	PRAMEF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005512.2	XM_496342	
PPARGC1A	10891	hgsc.bcm.edu	37	4	23815522	23815522	+	Silent	SNP	C	C	T	rs3755863	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr4:23815522C>T	ENST00000264867.2	-	8	1703	c.1584G>A	c.(1582-1584)acG>acA	p.T528T	PPARGC1A_ENST00000509702.1_5'UTR	NM_013261.3	NP_037393.1	Q9UBK2	PRGC1_HUMAN	peroxisome proliferator-activated receptor gamma, coactivator 1 alpha	528	Mediates interaction with RNF34. {ECO:0000269|PubMed:22064484}.				androgen metabolic process (GO:0008209)|androgen receptor signaling pathway (GO:0030521)|brown fat cell differentiation (GO:0050873)|cellular glucose homeostasis (GO:0001678)|cellular respiration (GO:0045333)|cellular response to fatty acid (GO:0071398)|cellular response to hypoxia (GO:0071456)|cellular response to nitrite (GO:0071250)|cellular response to oxidative stress (GO:0034599)|cellular response to thyroid hormone stimulus (GO:0097067)|cellular response to tumor necrosis factor (GO:0071356)|circadian regulation of gene expression (GO:0032922)|digestion (GO:0007586)|fatty acid oxidation (GO:0019395)|flavone metabolic process (GO:0051552)|galactose metabolic process (GO:0006012)|gluconeogenesis (GO:0006094)|mitochondrion organization (GO:0007005)|mRNA processing (GO:0006397)|negative regulation of glycolytic process (GO:0045820)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of neuron death (GO:1901215)|negative regulation of receptor activity (GO:2000272)|positive regulation of ATP biosynthetic process (GO:2001171)|positive regulation of cellular respiration (GO:1901857)|positive regulation of energy homeostasis (GO:2000507)|positive regulation of fatty acid oxidation (GO:0046321)|positive regulation of gluconeogenesis (GO:0045722)|positive regulation of histone acetylation (GO:0035066)|positive regulation of mitochondrial DNA metabolic process (GO:1901860)|positive regulation of mitochondrion organization (GO:0010822)|positive regulation of muscle tissue development (GO:1901863)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein stabilization (GO:0050821)|regulation of circadian rhythm (GO:0042752)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of transcription, DNA-templated (GO:0006355)|respiratory electron transport chain (GO:0022904)|response to cold (GO:0009409)|response to epinephrine (GO:0071871)|response to leucine (GO:0043201)|response to muscle activity (GO:0014850)|response to norepinephrine (GO:0071873)|response to starvation (GO:0042594)|response to statin (GO:0036273)|RNA splicing (GO:0008380)|temperature homeostasis (GO:0001659)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytosol (GO:0005829)|DNA-directed RNA polymerase II, core complex (GO:0005665)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin DNA binding (GO:0031490)|DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)|RNA polymerase II transcription cofactor activity (GO:0001104)|sequence-specific DNA binding (GO:0043565)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(7)|liver(1)|lung(24)|ovary(3)|skin(5)	51		Breast(46;0.0503)				AATAGGATTGCGTGCCATCCC	0.408													C|||	1764	0.352236	0.239	0.3343	5008	,	,		19235	0.4454		0.4284	False		,,,				2504	0.3436				p.T528T	Esophageal Squamous(29;694 744 13796 34866 44181)	Atlas-SNP	.											PPARGC1A,colon,carcinoma,0,1	PPARGC1A	129	1	0			c.G1584A	GRCh37	CM035706	PPARGC1A	M	rs3755863	PASS	.	C		1052,3354	384.2+/-325.2	120,812,1271	145.0	138.0	140.0		1584	3.2	1.0	4	dbSNP_107	140	3512,5088	512.9+/-378.0	695,2122,1483	no	coding-synonymous	PPARGC1A	NM_013261.3		815,2934,2754	TT,TC,CC		40.8372,23.8765,35.0915		528/799	23815522	4564,8442	2203	4300	6503	SO:0001819	synonymous_variant	10891	exon8			GGATTGCGTGCCA	AF106698	CCDS3429.1	4p15.1	2013-02-12	2006-10-17	2004-02-04	ENSG00000109819	ENSG00000109819		"""RNA binding motif (RRM) containing"""	9237	protein-coding gene	gene with protein product		604517	"""peroxisome proliferative activated receptor, gamma, coactivator 1"", ""peroxisome proliferative activated receptor, gamma, coactivator 1, alpha"""	PPARGC1		10585775	Standard	NM_013261		Approved	PGC1, PGC1A	uc003gqs.3	Q9UBK2	OTTHUMG00000097747	ENST00000264867.2:c.1584G>A	4.37:g.23815522C>T		Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	152	7	0.0460526	NM_013261	B7Z406|G8DM16|I3RTT5|I3RTT6|I3RTT7|I3RTT8|I3RTT9|Q3LIG1|Q4W5M7|Q9UN32	Silent	SNP	ENST00000264867.2	37	CCDS3429.1																																																																																			C|0.640;T|0.360	0.360	strong		0.408	PPARGC1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214976.1	NM_013261	
SNPH	9751	hgsc.bcm.edu	37	20	1285933	1285933	+	Silent	SNP	G	G	A	rs3795139	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr20:1285933G>A	ENST00000381873.3	+	6	956	c.720G>A	c.(718-720)ggG>ggA	p.G240G	SNPH_ENST00000381867.1_Silent_p.G284G	NM_014723.2	NP_055538.2	O15079	SNPH_HUMAN	syntaphilin	240					brain development (GO:0007420)|neuron differentiation (GO:0030182)|neurotransmitter secretion (GO:0007269)|synaptic vesicle docking involved in exocytosis (GO:0016081)	cell junction (GO:0030054)|cytoplasmic microtubule (GO:0005881)|integral component of membrane (GO:0016021)|mitochondrial membrane (GO:0031966)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|presynaptic membrane (GO:0042734)	syntaxin-1 binding (GO:0017075)			endometrium(2)|large_intestine(4)|lung(10)|ovary(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23						CTGAGGATGGGGCAGACAGTG	0.672													G|||	1973	0.39397	0.3979	0.3314	5008	,	,		17209	0.5407		0.3201	False		,,,				2504	0.3579				p.G240G		Atlas-SNP	.											.	SNPH	89	.	0			c.G720A						PASS	.	G		1676,2726		316,1044,841	27.0	27.0	27.0		720	-0.2	0.4	20	dbSNP_107	27	2477,6113		357,1763,2175	no	coding-synonymous	SNPH	NM_014723.2		673,2807,3016	AA,AG,GG		28.8359,38.0736,31.9658		240/495	1285933	4153,8839	2201	4295	6496	SO:0001819	synonymous_variant	9751	exon6			GGATGGGGCAGAC		CCDS13012.1	20p13	2008-07-02			ENSG00000101298	ENSG00000101298			15931	protein-coding gene	gene with protein product		604942				10707983	Standard	NM_014723		Approved	bA314N13.5	uc002wes.3	O15079	OTTHUMG00000031662	ENST00000381873.3:c.720G>A	20.37:g.1285933G>A		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	57	6	0.105263	NM_014723	Q8IYI3	Silent	SNP	ENST00000381873.3	37	CCDS13012.1																																																																																			G|0.650;A|0.350	0.350	strong		0.672	SNPH-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000145240.2	NM_014723	
ZNF763	284390	hgsc.bcm.edu	37	19	12087921	12087921	+	Silent	SNP	G	G	C	rs376310072	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr19:12087921G>C	ENST00000358987.3	+	2	199	c.72G>C	c.(70-72)tcG>tcC	p.S24S	ZNF763_ENST00000538752.1_Silent_p.S44S|ZNF763_ENST00000592625.1_Silent_p.S24S|ZNF763_ENST00000591944.1_Silent_p.S93S|ZNF763_ENST00000590798.1_Silent_p.S44S|ZNF763_ENST00000343949.5_Silent_p.S27S|ZNF763_ENST00000545530.1_Intron			Q0D2J5	ZN763_HUMAN	zinc finger protein 763	24	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(9)	15						TGGATATTTCGCAGAGGAAAC	0.493													N|||	4	0.000798722	0.0023	0.0	5008	,	,		18630	0.0		0.001	False		,,,				2504	0.0				p.S27S		Atlas-SNP	.											ZNF763,NS,carcinoma,+1,2	ZNF763	31	2	0			c.G81C						scavenged	.						150.0	152.0	151.0					19																	12087921		2203	4300	6503	SO:0001819	synonymous_variant	284390	exon2			TATTTCGCAGAGG	AK092240	CCDS45982.1	19p13.2	2014-02-12	2006-08-14		ENSG00000197054	ENSG00000197054		"""Zinc fingers, C2H2-type"", ""-"""	27614	protein-coding gene	gene with protein product							Standard	NM_001012753		Approved	ZNF440L		Q0D2J5	OTTHUMG00000156430	ENST00000358987.3:c.72G>C	19.37:g.12087921G>C		Somatic	214	5	0.0233645		WXS	Illumina HiSeq	Phase_I	232	15	0.0646552	NM_001012753	B3KRU3|B4DRE7	Silent	SNP	ENST00000358987.3	37																																																																																				.	.	alt		0.493	ZNF763-002	KNOWN	basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000344158.1	NM_001012753	
IPO5	3843	hgsc.bcm.edu	37	13	98670828	98670828	+	Silent	SNP	C	C	T	rs140767528	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr13:98670828C>T	ENST00000490680.1	+	23	2771	c.2706C>T	c.(2704-2706)taC>taT	p.Y902Y	IPO5_ENST00000539640.1_Silent_p.Y777Y|IPO5_ENST00000261574.5_Silent_p.Y920Y			O00410	IPO5_HUMAN	importin 5	902					cellular response to amino acid stimulus (GO:0071230)|negative regulation of catalytic activity (GO:0043086)|NLS-bearing protein import into nucleus (GO:0006607)|positive regulation of protein import into nucleus (GO:0042307)|ribosomal protein import into nucleus (GO:0006610)|viral process (GO:0016032)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	GTPase inhibitor activity (GO:0005095)|poly(A) RNA binding (GO:0044822)|protein transporter activity (GO:0008565)|Ran GTPase binding (GO:0008536)	p.Y920Y(1)		breast(2)|endometrium(2)|large_intestine(8)|lung(8)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	27						CATTTAAATACGCAGAATATT	0.443													T|||	9	0.00179712	0.0	0.0	5008	,	,		20116	0.0089		0.0	False		,,,				2504	0.0				p.Y920Y		Atlas-SNP	.											IPO5,colon,carcinoma,0,1	IPO5	90	1	1	Substitution - coding silent(1)	large_intestine(1)	c.C2760T						scavenged	.						162.0	145.0	151.0					13																	98670828		2203	4300	6503	SO:0001819	synonymous_variant	3843	exon26			TAAATACGCAGAA	U72761	CCDS31999.1	13q32.2	2012-05-02	2008-04-15	2008-04-15	ENSG00000065150	ENSG00000065150		"""Importins"""	6402	protein-coding gene	gene with protein product		602008	"""karyopherin (importin) beta 3"", ""RAN binding protein 5"""	KPNB3, RANBP5		9114010, 9271386, 17005651	Standard	NM_002271		Approved	IMB3, MGC2068, Pse1	uc001vne.3	O00410	OTTHUMG00000017244	ENST00000490680.1:c.2706C>T	13.37:g.98670828C>T		Somatic	213	1	0.00469484		WXS	Illumina HiSeq	Phase_I	192	4	0.0208333	NM_002271	B4DZA0|O15257|Q5T578|Q86XC7	Silent	SNP	ENST00000490680.1	37		9	0.004120879120879121	0	0.0	0	0.0	9	0.015734265734265736	0	0.0	T	9.160	1.018361	0.19355	.	.	ENSG00000065150	ENST00000469360	.	.	.	5.92	-3.57	0.04612	.	.	.	.	.	T	0.50480	0.1618	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.63681	-0.6582	4	.	.	.	-8.5326	16.364	0.83307	0.0:0.5025:0.0:0.4975	.	.	.	.	M	904	.	.	T	+	2	0	IPO5	97468829	0.718000	0.27976	0.975000	0.42487	0.995000	0.86356	-0.182000	0.09726	-0.649000	0.05430	-0.269000	0.10298	ACG	C|0.997;T|0.003	0.003	strong		0.443	IPO5-006	NOVEL	alternative_5_UTR|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000354655.1	NM_002271	
RIMS2	9699	hgsc.bcm.edu	37	8	104831794	104831794	+	Missense_Mutation	SNP	T	T	G			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr8:104831794T>G	ENST00000507740.1	+	1	295	c.59T>G	c.(58-60)gTt>gGt	p.V20G	RIMS2_ENST00000522174.1_3'UTR|RIMS2_ENST00000262231.10_Missense_Mutation_p.V20G|RIMS2_ENST00000406091.3_Intron	NM_014677.4	NP_055492.3	Q9UQ26	RIMS2_HUMAN	regulating synaptic membrane exocytosis 2	0					calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|cAMP-mediated signaling (GO:0019933)|insulin secretion (GO:0030073)|intracellular protein transport (GO:0006886)|positive regulation of gene expression (GO:0010628)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|regulation of exocytosis (GO:0017157)	cell junction (GO:0030054)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)	metal ion binding (GO:0046872)	p.S22fs*10(1)		NS(1)|breast(4)|central_nervous_system(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(22)|liver(1)|lung(68)|ovary(6)|pancreas(2)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(10)|urinary_tract(1)	144			OV - Ovarian serous cystadenocarcinoma(57;7.7e-07)|STAD - Stomach adenocarcinoma(118;0.229)			TTTCATGGGGTTTTTTCATCC	0.343										HNSCC(12;0.0054)																											p.V20G		Atlas-SNP	.											RIMS2_ENST00000507740,colon,carcinoma,+1,1	RIMS2	1357	1	1	Insertion - Frameshift(1)	large_intestine(1)	c.T59G						scavenged	.						103.0	102.0	102.0					8																	104831794		1813	4086	5899	SO:0001583	missense	9699	exon1			ATGGGGTTTTTTC	AB018294	CCDS43761.1, CCDS64948.1, CCDS64949.1	8q22.3	2008-08-08	2002-06-12	2002-06-14					17283	protein-coding gene	gene with protein product		606630	"""RAB3 interacting protein 3"""	RAB3IP3		9872452, 12578829	Standard	NM_014677		Approved	KIAA0751, RIM2, OBOE	uc003ylp.3	Q9UQ26		ENST00000507740.1:c.59T>G	8.37:g.104831794T>G	ENSP00000423559:p.Val20Gly	Somatic	114	1	0.00877193		WXS	Illumina HiSeq	Phase_I	84	22	0.261905	NM_014677	B3KX91|F8WD47|O43413|Q86XL9|Q8IWV9|Q8IWW1	Missense_Mutation	SNP	ENST00000507740.1	37	CCDS43761.1	.	.	.	.	.	.	.	.	.	.	T	15.55	2.865849	0.51588	.	.	ENSG00000176406	ENST00000515551;ENST00000262231;ENST00000507740;ENST00000408894	T;T;T;T	0.21932	1.98;2.04;2.05;1.99	5.71	5.71	0.89125	.	.	.	.	.	T	0.11879	0.0289	N	0.08118	0	0.80722	D	1	B;B	0.22683	0.073;0.073	B;B	0.24701	0.055;0.055	T	0.14587	-1.0467	9	0.39692	T	0.17	.	10.3403	0.43873	0.0:0.0731:0.0:0.9269	.	20;20	Q9UQ26-1;Q9UQ26-3	.;.	G	20	ENSP00000425205:V20G;ENSP00000262231:V20G;ENSP00000423559:V20G;ENSP00000386228:V20G	ENSP00000262231:V20G	V	+	2	0	RIMS2	104900970	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.646000	0.61411	2.168000	0.68352	0.477000	0.44152	GTT	.	.	none		0.343	RIMS2-005	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367215.1	NM_001100117	
CARD6	84674	hgsc.bcm.edu	37	5	40853048	40853048	+	Silent	SNP	C	C	T	rs16870407	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr5:40853048C>T	ENST00000254691.5	+	3	1813	c.1614C>T	c.(1612-1614)agC>agT	p.S538S	CARD6_ENST00000381677.3_Intron	NM_032587.3	NP_115976.2	Q9BX69	CARD6_HUMAN	caspase recruitment domain family, member 6	538					apoptotic process (GO:0006915)|regulation of apoptotic process (GO:0042981)					NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|liver(2)|lung(29)|ovary(2)|pancreas(1)|prostate(2)|skin(3)|urinary_tract(1)	62						ATCTAGAAAGCTTTTGGACTC	0.388													C|||	827	0.165136	0.0295	0.1974	5008	,	,		20396	0.3284		0.0805	False		,,,				2504	0.2444				p.S538S		Atlas-SNP	.											CARD6,caecum,carcinoma,+1,1	CARD6	141	1	0			c.C1614T						scavenged	.	C		217,4189	124.1+/-161.4	5,207,1991	90.0	97.0	95.0		1614	1.2	0.3	5	dbSNP_123	95	798,7802	174.0+/-224.4	47,704,3549	no	coding-synonymous	CARD6	NM_032587.3		52,911,5540	TT,TC,CC		9.2791,4.9251,7.8041		538/1038	40853048	1015,11991	2203	4300	6503	SO:0001819	synonymous_variant	84674	exon3			AGAAAGCTTTTGG	AF356193	CCDS3935.1	5p13.1	2008-05-23			ENSG00000132357	ENSG00000132357			16394	protein-coding gene	gene with protein product		609986				12775719	Standard	NM_032587		Approved	CINCIN1	uc003jmg.3	Q9BX69	OTTHUMG00000094775	ENST00000254691.5:c.1614C>T	5.37:g.40853048C>T		Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	130	5	0.0384615	NM_032587	Q52LR2	Silent	SNP	ENST00000254691.5	37	CCDS3935.1																																																																																			C|0.892;G|0.000;T|0.108	0.108	strong		0.388	CARD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211584.3		
LMBRD1	55788	hgsc.bcm.edu	37	6	70409081	70409081	+	Missense_Mutation	SNP	A	A	G	rs185334169	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr6:70409081A>G	ENST00000370577.3	-	13	1421	c.1192T>C	c.(1192-1194)Tat>Cat	p.Y398H	LMBRD1_ENST00000370570.1_Missense_Mutation_p.Y325H	NM_018368.3	NP_060838.3	Q9NUN5	LMBD1_HUMAN	LMBR1 domain containing 1	398					cobalamin metabolic process (GO:0009235)|insulin receptor internalization (GO:0038016)|negative regulation of glucose import (GO:0046325)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of protein kinase B signaling (GO:0051898)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	clathrin-coated endocytic vesicle (GO:0045334)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cobalamin binding (GO:0031419)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(7)|lung(11)|ovary(2)|upper_aerodigestive_tract(1)	31						CTGATTTTATATAACTGGAAA	0.333													A|||	9	0.00179712	0.0	0.0	5008	,	,		14747	0.0079		0.0	False		,,,				2504	0.001				p.Y398H		Atlas-SNP	.											.	LMBRD1	61	.	0			c.T1192C						PASS	.						95.0	102.0	100.0					6																	70409081		2203	4300	6503	SO:0001583	missense	55788	exon13			TTTTATATAACTG	AF113224	CCDS4969.1	6q13	2011-05-12	2005-07-25	2005-07-25	ENSG00000168216	ENSG00000168216			23038	protein-coding gene	gene with protein product		612625	"""chromosome 6 open reading frame 209"""	C6orf209		19136951	Standard	NM_018368		Approved	FLJ11240, bA810I22.1, cblF	uc003pfa.3	Q9NUN5	OTTHUMG00000014985	ENST00000370577.3:c.1192T>C	6.37:g.70409081A>G	ENSP00000359609:p.Tyr398His	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	107	7	0.0654206	NM_018368	A8K204|E1P531|Q5VUN6|Q86Y70|Q96FW4|Q9BY56|Q9NZD6	Missense_Mutation	SNP	ENST00000370577.3	37	CCDS4969.1	7	0.003205128205128205	0	0.0	0	0.0	7	0.012237762237762238	0	0.0	A	21.8	4.197829	0.79015	.	.	ENSG00000168216	ENST00000370577;ENST00000370570	T;T	0.18502	2.21;2.21	5.23	5.23	0.72850	.	0.000000	0.85682	D	0.000000	T	0.19525	0.0469	L	0.49350	1.555	0.80722	D	1	D	0.76494	0.999	D	0.66196	0.942	T	0.04767	-1.0928	10	0.11182	T	0.66	-11.6488	15.4018	0.74845	1.0:0.0:0.0:0.0	.	398	Q9NUN5	LMBD1_HUMAN	H	398;325	ENSP00000359609:Y398H;ENSP00000359602:Y325H	ENSP00000359602:Y325H	Y	-	1	0	LMBRD1	70465802	1.000000	0.71417	1.000000	0.80357	0.906000	0.53458	9.244000	0.95423	2.095000	0.63458	0.482000	0.46254	TAT	A|0.997;G|0.003	0.003	strong		0.333	LMBRD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041124.1	NM_018368	
CHMP2B	25978	hgsc.bcm.edu	37	3	87276699	87276699	+	Silent	SNP	C	C	T	rs2279720	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr3:87276699C>T	ENST00000263780.4	+	1	265	c.27C>T	c.(25-27)acC>acT	p.T9T	CHMP2B_ENST00000472024.1_3'UTR|MIR4795_ENST00000584182.1_RNA|CHMP2B_ENST00000471660.1_5'UTR|CHMP2B_ENST00000494980.1_Silent_p.T9T	NM_014043.3	NP_054762.2	Q9UQN3	CHM2B_HUMAN	charged multivesicular body protein 2B	9					cell death (GO:0008219)|endosomal transport (GO:0016197)|membrane organization (GO:0061024)|protein transport (GO:0015031)|viral life cycle (GO:0019058)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	protein domain specific binding (GO:0019904)			NS(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(1)|ovary(1)|skin(2)	12	all_cancers(8;0.104)|Lung SC(3;0.184)	Lung NSC(201;0.0777)		LUSC - Lung squamous cell carcinoma(29;0.00241)|Lung(72;0.00712)		AGAAGAAAACCGTGGATGGTG	0.642													C|||	537	0.107228	0.1112	0.0692	5008	,	,		15188	0.1875		0.0696	False		,,,				2504	0.0849				p.T9T		Atlas-SNP	.											CHMP2B,NS,carcinoma,0,1	CHMP2B	28	1	0			c.C27T						PASS	.	C		458,3948	215.5+/-234.4	21,416,1766	61.0	71.0	67.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	27	1.0	1.0	3	dbSNP_100	67	758,7842	180.6+/-229.5	39,680,3581	no	coding-synonymous	CHMP2B	NM_014043.3		60,1096,5347	TT,TC,CC		8.814,10.3949,9.3495		9/214	87276699	1216,11790	2203	4300	6503	SO:0001819	synonymous_variant	25978	exon1			GAAAACCGTGGAT	BC001553	CCDS2918.1, CCDS58840.1	3p12.1	2011-09-21	2011-09-21		ENSG00000083937	ENSG00000083937		"""Charged multivesicular body proteins"""	24537	protein-coding gene	gene with protein product	"""VPS2 homolog B (S. cerevisiae)"""	609512	"""chromatin modifying protein 2B"""			11559748	Standard	NM_014043		Approved	DKFZP564O123, CHMP2.5, VPS2B	uc003dqp.4	Q9UQN3	OTTHUMG00000158982	ENST00000263780.4:c.27C>T	3.37:g.87276699C>T		Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	144	8	0.0555556	NM_014043	B4DJG8|Q53HC7|Q9Y4U6	Silent	SNP	ENST00000263780.4	37	CCDS2918.1																																																																																			C|0.889;T|0.111	0.111	strong		0.642	CHMP2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352779.2	NM_014043	
UBQLN1	29979	hgsc.bcm.edu	37	9	86278817	86278817	+	Silent	SNP	C	C	A	rs7866234	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr9:86278817C>A	ENST00000376395.4	-	10	2113	c.1590G>T	c.(1588-1590)ctG>ctT	p.L530L	UBQLN1_ENST00000257468.7_Silent_p.L502L	NM_013438.4|NM_053067.2	NP_038466.2|NP_444295.1	Q9UMX0	UBQL1_HUMAN	ubiquilin 1	530					cellular response to hypoxia (GO:0071456)|regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902175)|regulation of protein ubiquitination (GO:0031396)|response to endoplasmic reticulum stress (GO:0034976)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|proteasome complex (GO:0000502)|protein complex (GO:0043234)	kinase binding (GO:0019900)			breast(4)|endometrium(2)|kidney(4)|large_intestine(6)|lung(10)|prostate(1)	27						CAAGAGCCTGCAGCATCTGCT	0.413													C|||	1927	0.384784	0.2005	0.4164	5008	,	,		17810	0.8075		0.2217	False		,,,				2504	0.3436				p.L530L	Melanoma(186;1284 2073 12755 14558 18426)	Atlas-SNP	.											.	UBQLN1	49	.	0			c.G1590T						PASS	.	C	,	895,3511	347.5+/-309.5	92,711,1400	157.0	143.0	148.0		1590,1506	-0.4	1.0	9	dbSNP_116	148	2031,6569	354.0+/-329.3	225,1581,2494	no	coding-synonymous,coding-synonymous	UBQLN1	NM_013438.4,NM_053067.2	,	317,2292,3894	AA,AC,CC		23.6163,20.3132,22.4973	,	530/590,502/562	86278817	2926,10080	2203	4300	6503	SO:0001819	synonymous_variant	29979	exon10			AGCCTGCAGCATC	AF176069	CCDS6663.1, CCDS6664.1	9q22	2013-02-12			ENSG00000135018	ENSG00000135018		"""Ubiquilin family"""	12508	protein-coding gene	gene with protein product		605046				9303440, 10807547	Standard	NM_013438		Approved	DSK2, PLIC-1, XDRP1, DA41	uc004amv.3	Q9UMX0	OTTHUMG00000020104	ENST00000376395.4:c.1590G>T	9.37:g.86278817C>A		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	121	11	0.0909091	NM_013438	Q5T6J5|Q5T6J9|Q8IXS9|Q8N2Q3|Q9H0T8|Q9H3R4|Q9HAZ5	Silent	SNP	ENST00000376395.4	37	CCDS6663.1	878	0.40201465201465203	105	0.21341463414634146	143	0.39502762430939226	454	0.7937062937062938	176	0.23218997361477572	C	5.480	0.273549	0.10403	0.203132	0.236163	ENSG00000135018	ENST00000526134	.	.	.	5.74	-0.392	0.12442	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.29181	-1.0020	3	.	.	.	.	12.9536	0.58415	0.0:0.7091:0.0:0.2909	rs7866234;rs60840479;rs7866234	.	.	.	F	137	.	.	C	-	2	0	UBQLN1	85468637	0.959000	0.32827	0.985000	0.45067	0.631000	0.37964	0.036000	0.13819	-0.369000	0.08028	-1.708000	0.00717	TGC	C|0.700;A|0.300	0.300	strong		0.413	UBQLN1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000052834.1	NM_013438	
OR13C5	138799	hgsc.bcm.edu	37	9	107360922	107360922	+	Missense_Mutation	SNP	A	A	G	rs1851724	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr9:107360922A>G	ENST00000374779.2	-	1	866	c.773T>C	c.(772-774)aTg>aCg	p.M258T		NM_001004482.1	NP_001004482.1	Q8NGS8	O13C5_HUMAN	olfactory receptor, family 13, subfamily C, member 5	258			M -> T (in dbSNP:rs1851724).			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(1)|large_intestine(2)|lung(11)|ovary(2)|pancreas(2)|prostate(2)|skin(4)	28						CTTCATGTACATGAGGAAGAT	0.443													A|||	3390	0.676917	0.7466	0.5937	5008	,	,		20659	0.9573		0.4235	False		,,,				2504	0.6135				p.M258T		Atlas-SNP	.											OR13C5,NS,lymphoid_neoplasm,0,1	OR13C5	60	1	0			c.T773C						scavenged	.	A	THR/MET	3165,1241	706.6+/-407.4	1144,877,182	137.0	123.0	128.0		773	4.0	0.9	9	dbSNP_92	128	3648,4952	525.3+/-380.7	806,2036,1458	yes	missense	OR13C5	NM_001004482.1	81	1950,2913,1640	GG,GA,AA		42.4186,28.1661,47.6165	possibly-damaging	258/319	107360922	6813,6193	2203	4300	6503	SO:0001583	missense	138799	exon1			ATGTACATGAGGA		CCDS35091.1	9q31.1	2012-10-03			ENSG00000255800	ENSG00000277556		"""GPCR / Class A : Olfactory receptors"""	15100	protein-coding gene	gene with protein product							Standard	NM_001004482		Approved		uc011lvp.2	Q8NGS8	OTTHUMG00000020408	ENST00000374779.2:c.773T>C	9.37:g.107360922A>G	ENSP00000363911:p.Met258Thr	Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	191	5	0.026178	NM_001004482	B2RNE5|B9EGW5|Q6IF53	Missense_Mutation	SNP	ENST00000374779.2	37	CCDS35091.1	1440	0.6593406593406593	349	0.709349593495935	207	0.5718232044198895	550	0.9615384615384616	334	0.44063324538258575	A	14.53	2.562208	0.45694	0.718339	0.424186	ENSG00000255800	ENST00000374779	T	0.00164	8.64	4.03	4.03	0.46877	GPCR, rhodopsin-like superfamily (1);	0.395212	0.18447	U	0.140947	T	0.00012	0.0000	L	0.41492	1.28	0.45806	P	0.0013180000000000414	P	0.39601	0.68	P	0.45406	0.479	T	0.48536	-0.9027	9	0.51188	T	0.08	.	6.0217	0.19632	0.8838:0.0:0.1162:0.0	rs1851724;rs52797012;rs61541229;rs1851724	258	Q8NGS8	O13C5_HUMAN	T	258	ENSP00000363911:M258T	ENSP00000363911:M258T	M	-	2	0	OR13C5	106400743	0.036000	0.19791	0.947000	0.38551	0.290000	0.27261	1.107000	0.31110	1.704000	0.51252	0.347000	0.21830	ATG	A|0.421;G|0.579	0.579	strong		0.443	OR13C5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053479.2	NM_001004482	
CMYA5	202333	hgsc.bcm.edu	37	5	79031372	79031372	+	Missense_Mutation	SNP	G	G	C	rs6859595	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr5:79031372G>C	ENST00000446378.2	+	2	6815	c.6784G>C	c.(6784-6786)Gtt>Ctt	p.V2262L		NM_153610.3	NP_705838.3	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	2262			V -> L (in dbSNP:rs6859595). {ECO:0000269|PubMed:15489334}.		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)		CGGTCAAAACGTTAAAGAAAA	0.343													G|||	1359	0.271366	0.5749	0.0821	5008	,	,		20192	0.3621		0.0815	False		,,,				2504	0.0971				p.V2262L		Atlas-SNP	.											.	CMYA5	643	.	0			c.G6784C						PASS	.	G	LEU/VAL	1758,1834		439,880,477	68.0	71.0	70.0		6784	-1.3	0.9	5	dbSNP_116	70	697,7435		40,617,3409	yes	missense	CMYA5	NM_153610.3	32	479,1497,3886	CC,CG,GG		8.5711,48.9421,20.94	benign	2262/4070	79031372	2455,9269	1796	4066	5862	SO:0001583	missense	202333	exon2			CAAAACGTTAAAG	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.6784G>C	5.37:g.79031372G>C	ENSP00000394770:p.Val2262Leu	Somatic	229	0	0		WXS	Illumina HiSeq	Phase_I	215	9	0.0418605	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	620	0.2838827838827839	299	0.6077235772357723	30	0.08287292817679558	232	0.40559440559440557	59	0.07783641160949868	G	0.005	-2.236224	0.00277	0.489421	0.085711	ENSG00000164309	ENST00000446378	T	0.15017	2.46	5.74	-1.29	0.09288	.	0.951459	0.08743	N	0.900308	T	0.00012	0.0000	N	0.11427	0.14	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.47032	-0.9148	9	0.02654	T	1	.	1.4302	0.02332	0.1568:0.2929:0.3491:0.2012	rs6859595;rs17846621;rs17859711;rs57126049;rs6859595	2262	Q8N3K9	CMYA5_HUMAN	L	2262	ENSP00000394770:V2262L	ENSP00000394770:V2262L	V	+	1	0	CMYA5	79067128	0.002000	0.14202	0.943000	0.38184	0.004000	0.04260	-0.194000	0.09559	0.147000	0.19030	-1.149000	0.01842	GTT	G|0.737;C|0.263	0.263	strong		0.343	CMYA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369497.1	NM_153610	
CCDC178	374864	hgsc.bcm.edu	37	18	30804758	30804758	+	Missense_Mutation	SNP	A	A	C	rs457896|rs113589354|rs386802235	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr18:30804758A>C	ENST00000383096.3	-	17	1981	c.1799T>G	c.(1798-1800)cTc>cGc	p.L600R	CCDC178_ENST00000406524.2_Missense_Mutation_p.L600R|CCDC178_ENST00000300227.8_Missense_Mutation_p.L600R|CCDC178_ENST00000403303.1_Missense_Mutation_p.L600R|CCDC178_ENST00000579947.1_Missense_Mutation_p.L600R|CCDC178_ENST00000402325.1_Missense_Mutation_p.L600R|CCDC178_ENST00000583930.1_Missense_Mutation_p.L600R|CCDC178_ENST00000579916.1_Intron			Q5BJE1	CC178_HUMAN	coiled-coil domain containing 178	600			L -> R (in dbSNP:rs457896).														TTCTTTGTCGAGACTTCTGAT	0.328													A|||	823	0.164337	0.3517	0.1023	5008	,	,		15173	0.1121		0.1093	False		,,,				2504	0.0654				p.L600R		Atlas-SNP	.											C18orf34_ENST00000383096,colon,carcinoma,0,2	.	.	2	0			c.T1799G						scavenged	.	A	ARG/LEU,ARG/LEU	1272,3132		187,898,1117	74.0	71.0	72.0		1799,1799	-4.0	0.0	18	dbSNP_80	72	828,7772		39,750,3511	yes	missense,missense	C18orf34	NM_001105528.1,NM_198995.2	102,102	226,1648,4628	CC,CA,AA		9.6279,28.8828,16.1489	probably-damaging,probably-damaging	600/868,600/830	30804758	2100,10904	2202	4300	6502	SO:0001583	missense	374864	exon16			TTGTCGAGACTTC	AK126038	CCDS11906.1, CCDS42424.1	18q12.1	2012-10-15	2012-10-15	2012-10-15	ENSG00000166960	ENSG00000166960			29588	protein-coding gene	gene with protein product			"""chromosome 18 open reading frame 34"""	C18orf34			Standard	NM_198995		Approved	FLJ44050	uc002kxn.2	Q5BJE1	OTTHUMG00000132279	ENST00000383096.3:c.1799T>G	18.37:g.30804758A>C	ENSP00000372576:p.Leu600Arg	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	91	2	0.021978	NM_001105528	A6NDC6|J3KS92|Q6ZP67|Q6ZU20	Missense_Mutation	SNP	ENST00000383096.3	37	CCDS42424.1	342	0.1565934065934066	160	0.3252032520325203	36	0.09944751381215469	71	0.12412587412587413	75	0.09894459102902374	A	4.860	0.159803	0.09287	0.288828	0.096279	ENSG00000166960	ENST00000403303;ENST00000383096;ENST00000300227;ENST00000406524;ENST00000402325	T;T;T;T;T	0.19394	2.25;2.25;2.15;2.25;2.16	4.58	-3.98	0.04082	.	.	.	.	.	T	0.00012	0.0000	L	0.40543	1.245	0.80722	P	0.0	P;P;P;P;P	0.43094	0.799;0.799;0.799;0.799;0.799	B;B;B;B;B	0.39258	0.295;0.295;0.295;0.295;0.295	T	0.38757	-0.9646	8	0.23302	T	0.38	11.9035	7.1837	0.25786	0.3349:0.1641:0.5009:0.0	rs457896;rs59393965;rs457896	600;600;600;600;600	F8W7A7;Q5BJE1-3;B5MD75;Q5BJE1-2;Q5BJE1	.;.;.;.;CR034_HUMAN	R	600	ENSP00000385591:L600R;ENSP00000372576:L600R;ENSP00000300227:L600R;ENSP00000385867:L600R;ENSP00000385234:L600R	ENSP00000300227:L600R	L	-	2	0	C18orf34	29058756	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.025000	0.13577	-0.699000	0.05077	-0.297000	0.09499	CTC	A|0.836;C|0.164	0.164	strong		0.328	CCDC178-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255373.2	NM_198995	
C4A	720	hgsc.bcm.edu	37	6	31963559	31963559	+	Missense_Mutation	SNP	A	A	G	rs147162052		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr6:31963559A>G	ENST00000428956.2	+	25	3302	c.3218A>G	c.(3217-3219)gAc>gGc	p.D1073G	C4A_ENST00000498271.1_Missense_Mutation_p.D1073G	NM_007293.2	NP_009224.2	P0C0L4	CO4A_HUMAN	complement component 4A (Rodgers blood group)	1073			D -> G (in allotype C4A1, allotype C4A2; dbSNP:rs147162052). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:3696167, ECO:0000269|Ref.8}.		complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of apoptotic cell clearance (GO:2000427)|regulation of complement activation (GO:0030449)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	complement component C1q binding (GO:0001849)|endopeptidase inhibitor activity (GO:0004866)									Intravenous Immunoglobulin(DB00028)	TTGTCACGGGACAGCAGCACC	0.612																																					p.G1073G		Atlas-SNP	.											C4B,right_upper_lobe,carcinoma,0,2	C4A	15	2	0			c.G3218G						scavenged	.						101.0	86.0	91.0					6																	31963559		1499	2656	4155	SO:0001583	missense	720	exon25			CACGGGACAGCAG	L26261, M14823, X77491, AY224378	CCDS47404.1, CCDS59005.1	6p21.3	2014-09-17	2006-01-19		ENSG00000244731	ENSG00000244731		"""Blood group antigens"", ""Complement system"""	1323	protein-coding gene	gene with protein product		120810	"""complement component 4A"""				Standard	NM_001252204		Approved	CPAMD2, C4S, CO4, C4, C4A3, C4A2, C4A4, C4A6, C4B, RG		P0C0L4	OTTHUMG00000031186	ENST00000428956.2:c.3218A>G	6.37:g.31963559A>G	ENSP00000396688:p.Asp1073Gly	Somatic	515	6	0.0116505		WXS	Illumina HiSeq	Phase_I	579	9	0.015544	NM_007293	A6H8M8|A6NHJ5|A7E2V2|B0QZR6|B0V2C8|B2RUT6|B7ZVZ6|P01028|P78445|Q13160|Q13906|Q14033|Q14835|Q4LE82|Q5JNX2|Q5JQM8|Q6P4R1|Q6U2E5|Q6U2E8|Q6U2F0|Q6U2F3|Q6U2F4|Q6U2F6|Q6U2F8|Q6U2G0|Q96EG2|Q96SA8|Q9NPK5|Q9UIP5	Silent	SNP	ENST00000428956.2	37	CCDS47404.1	.	.	.	.	.	.	.	.	.	.	A	1.712	-0.498842	0.04291	.	.	ENSG00000244731	ENST00000428956;ENST00000498271	T;T	0.37915	1.17;1.17	3.11	1.88	0.25563	Terpenoid cylases/protein prenyltransferase alpha-alpha toroid (1);A-macroglobulin complement component (1);	.	.	.	.	T	0.16642	0.0400	M	0.64170	1.965	0.80722	D	1	B;B	0.19200	0.015;0.034	B;B	0.23150	0.026;0.044	T	0.04885	-1.0920	9	0.46703	T	0.11	.	5.4739	0.16686	0.8606:0.0:0.1394:0.0	.	1073;1073	A6H8M8;P0C0L4	.;CO4A_HUMAN	G	1073	ENSP00000396688:D1073G;ENSP00000420212:D1073G	ENSP00000396688:D1073G	D	+	2	0	C4A	32071538	0.168000	0.22989	0.910000	0.35882	0.043000	0.13939	0.471000	0.22100	0.399000	0.25367	-1.226000	0.01582	GAC	A|0.500;G|0.500	0.500	strong		0.612	C4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076364.3	NM_007293	
EEF1A2	1917	hgsc.bcm.edu	37	20	62126299	62126299	+	Silent	SNP	C	C	T	rs2274860	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr20:62126299C>T	ENST00000298049.7	-	3	550	c.480G>A	c.(478-480)ccG>ccA	p.P160P	EEF1A2_ENST00000217182.3_Silent_p.P160P			Q05639	EF1A2_HUMAN	eukaryotic translation elongation factor 1 alpha 2	160	tr-type G.				positive regulation of apoptotic process (GO:0043065)|response to inorganic substance (GO:0010035)	eukaryotic translation elongation factor 1 complex (GO:0005853)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|translation elongation factor activity (GO:0003746)|translation factor activity, nucleic acid binding (GO:0008135)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(14)|stomach(1)	20	all_cancers(38;9.45e-12)		BRCA - Breast invasive adenocarcinoma(10;1.22e-05)			CGCTGTAGGCCGGCTCTGTGG	0.592													C|||	702	0.140176	0.0068	0.1095	5008	,	,		17708	0.4286		0.1392	False		,,,				2504	0.046				p.P160P		Atlas-SNP	.											.	EEF1A2	60	.	0			c.G480A						PASS	.	C		147,4255	101.2+/-139.8	1,145,2055	108.0	85.0	93.0		480	-7.7	0.4	20	dbSNP_100	93	1142,7458	234.4+/-267.4	78,986,3236	no	coding-synonymous	EEF1A2	NM_001958.2		79,1131,5291	TT,TC,CC		13.2791,3.3394,9.9139		160/464	62126299	1289,11713	2201	4300	6501	SO:0001819	synonymous_variant	1917	exon4			GTAGGCCGGCTCT	AF163763	CCDS13522.1	20q13.3	2010-06-03			ENSG00000101210	ENSG00000101210			3192	protein-coding gene	gene with protein product		602959	"""statin-like"", ""statin"""	STNL, STN		8354261, 8812466	Standard	NM_001958		Approved	EEF1AL, HS1	uc002yfe.2	Q05639	OTTHUMG00000033076	ENST00000298049.7:c.480G>A	20.37:g.62126299C>T		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	115	7	0.0608696	NM_001958	B5BUF3|E1P5J1|P54266|Q0VGC7	Silent	SNP	ENST00000298049.7	37	CCDS13522.1																																																																																			C|0.872;T|0.128	0.128	strong		0.592	EEF1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080495.1	NM_001958	
KDM3A	55818	hgsc.bcm.edu	37	2	86697366	86697366	+	Missense_Mutation	SNP	T	T	A	rs186664065	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr2:86697366T>A	ENST00000409556.1	+	12	1924	c.1559T>A	c.(1558-1560)cTc>cAc	p.L520H	KDM3A_ENST00000409064.1_Missense_Mutation_p.L520H|KDM3A_ENST00000542128.1_Missense_Mutation_p.L468H|KDM3A_ENST00000485171.1_3'UTR|KDM3A_ENST00000312912.5_Missense_Mutation_p.L520H			Q9Y4C1	KDM3A_HUMAN	lysine (K)-specific demethylase 3A	520					androgen receptor signaling pathway (GO:0030521)|formaldehyde biosynthetic process (GO:0046293)|histone H3-K9 demethylation (GO:0033169)|histone H3-K9 dimethylation (GO:0036123)|hormone-mediated signaling pathway (GO:0009755)|negative regulation of histone H3-K9 methylation (GO:0051573)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|spermatid nucleus elongation (GO:0007290)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|core promoter binding (GO:0001047)|dioxygenase activity (GO:0051213)|iron ion binding (GO:0005506)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region sequence-specific DNA binding (GO:0000976)	p.L520H(1)		NS(1)|breast(3)|central_nervous_system(2)|endometrium(5)|kidney(5)|large_intestine(7)|liver(1)|lung(13)|ovary(1)|prostate(3)|skin(1)|stomach(3)|upper_aerodigestive_tract(2)	47						CCAGCTAAACTCAAAAAGCTG	0.443													T|||	14	0.00279553	0.0	0.0	5008	,	,		18531	0.0139		0.0	False		,,,				2504	0.0				p.L520H	NSCLC(96;1150 1523 6936 46253 49736)	Atlas-SNP	.											KDM3A,NS,carcinoma,0,1	KDM3A	179	1	1	Substitution - Missense(1)	stomach(1)	c.T1559A						scavenged	.						97.0	92.0	94.0					2																	86697366		2203	4300	6503	SO:0001583	missense	55818	exon11			CTAAACTCAAAAA	AB018285	CCDS1990.1	2p11.2	2011-07-01	2009-04-06	2009-04-06	ENSG00000115548	ENSG00000115548		"""Chromatin-modifying enzymes / K-demethylases"""	20815	protein-coding gene	gene with protein product	"""jumonji C domain-containing histone demethylase 2A"""	611512	"""jumonji domain containing 1"", ""jumonji domain containing 1A"""	JMJD1, JMJD1A		9872452	Standard	NM_018433		Approved	TSGA, KIAA0742, JHMD2A	uc010ytj.2	Q9Y4C1	OTTHUMG00000130204	ENST00000409556.1:c.1559T>A	2.37:g.86697366T>A	ENSP00000386660:p.Leu520His	Somatic	259	1	0.003861		WXS	Illumina HiSeq	Phase_I	278	6	0.0215827	NM_001146688	D6W5M3|Q53S72|Q68D47|Q68UT9|Q6N050|Q8IY08	Missense_Mutation	SNP	ENST00000409556.1	37	CCDS1990.1	8	0.003663003663003663	0	0.0	0	0.0	8	0.013986013986013986	0	0.0	T	28.9	4.959103	0.92726	.	.	ENSG00000115548	ENST00000409556;ENST00000540058;ENST00000312912;ENST00000409064;ENST00000542128	T;T;T;T	0.51574	0.7;0.7;0.7;0.7	5.66	5.66	0.87406	.	0.521028	0.18414	N	0.141971	T	0.36552	0.0971	N	0.08118	0	0.39892	D	0.973789	D;D	0.54601	0.964;0.967	P;P	0.56700	0.804;0.642	T	0.54337	-0.8309	10	0.72032	D	0.01	.	15.065	0.71986	0.0:0.0:0.0:1.0	.	468;520	F5H070;Q9Y4C1	.;KDM3A_HUMAN	H	520;520;520;520;468	ENSP00000386660:L520H;ENSP00000323659:L520H;ENSP00000386516:L520H;ENSP00000438324:L468H	ENSP00000323659:L520H	L	+	2	0	KDM3A	86550877	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.823000	0.86660	2.158000	0.67659	0.533000	0.62120	CTC	T|0.996;A|0.004	0.004	strong		0.443	KDM3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252522.2	NM_018433	
CCP110	9738	hgsc.bcm.edu	37	16	19547747	19547747	+	Missense_Mutation	SNP	C	C	G	rs226891	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr16:19547747C>G	ENST00000381396.5	+	4	1003	c.756C>G	c.(754-756)atC>atG	p.I252M	CCP110_ENST00000396208.2_Missense_Mutation_p.I252M|CCP110_ENST00000396212.2_Missense_Mutation_p.I252M	NM_001199022.1	NP_001185951	O43303	CP110_HUMAN	centriolar coiled coil protein 110kDa	252			I -> M (in dbSNP:rs226891). {ECO:0000269|PubMed:10493829, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005, ECO:0000269|PubMed:9455477}.		cell projection organization (GO:0030030)|centriole replication (GO:0007099)|centrosome duplication (GO:0051298)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of cytokinesis (GO:0032465)	centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)|protein complex (GO:0043234)		p.I252M(1)		breast(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(8)|stomach(3)|urinary_tract(1)	21						GAGGTAGTATCAACAGAATTG	0.388													G|||	4147	0.828075	0.9637	0.8602	5008	,	,		20963	0.7579		0.9324	False		,,,				2504	0.5869				p.I252M		Atlas-SNP	.											CCP110,NS,carcinoma,0,1	CCP110	57	1	1	Substitution - Missense(1)	stomach(1)	c.C756G						scavenged	.	G	MET/ILE,MET/ILE	4165,229	134.5+/-170.7	1972,221,4	65.0	65.0	65.0		756,756	-7.8	0.0	16	dbSNP_79	65	7888,712	171.0+/-222.0	3613,662,25	yes	missense,missense	CCP110	NM_001199022.1,NM_014711.4	10,10	5585,883,29	GG,GC,CC		8.2791,5.2117,7.2418	benign,benign	252/1013,252/992	19547747	12053,941	2197	4300	6497	SO:0001583	missense	9738	exon4			TAGTATCAACAGA	AB007879	CCDS10579.1, CCDS55992.1	16p12.3	2014-02-20	2011-05-27		ENSG00000103540	ENSG00000103540			24342	protein-coding gene	gene with protein product		609544				9455477, 12361598, 16760425	Standard	NM_014711		Approved	KIAA0419, CP110	uc002dgl.4	O43303	OTTHUMG00000131459	ENST00000381396.5:c.756C>G	16.37:g.19547747C>G	ENSP00000370803:p.Ile252Met	Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	65	4	0.0615385	NM_001199022	B7WP23|O43335|Q68DV9|Q8NE13	Missense_Mutation	SNP	ENST00000381396.5	37	CCDS55992.1	1935	0.885989010989011	476	0.967479674796748	311	0.8591160220994475	449	0.784965034965035	699	0.9221635883905013	G	2.101	-0.406059	0.04832	0.947883	0.917209	ENSG00000103540	ENST00000396212;ENST00000381396;ENST00000396208	T;T;T	0.14266	2.52;2.53;2.52	5.89	-7.75	0.01236	.	1.516010	0.03430	N	0.207608	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B	0.13594	0.008;0.008	B;B	0.08055	0.002;0.003	T	0.34675	-0.9819	9	0.42905	T	0.14	-17.0742	3.376	0.07238	0.2849:0.3818:0.24:0.0933	rs226891;rs394162;rs17857124;rs52827190;rs61313075;rs226891	252;252	O43303;O43303-2	CP110_HUMAN;.	M	252	ENSP00000379515:I252M;ENSP00000370803:I252M;ENSP00000379511:I252M	ENSP00000370803:I252M	I	+	3	3	CCP110	19455248	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.056000	0.03489	-1.174000	0.02754	-1.093000	0.02169	ATC	C|0.098;G|0.902	0.902	strong		0.388	CCP110-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254284.2	NM_014711	
SERPINB5	5268	hgsc.bcm.edu	37	18	61160320	61160320	+	Missense_Mutation	SNP	G	G	C	rs2289520	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr18:61160320G>C	ENST00000382771.4	+	5	851	c.559G>C	c.(559-561)Gtc>Ctc	p.V187L	SERPINB5_ENST00000489441.1_Missense_Mutation_p.V187L|SERPINB5_ENST00000464346.1_3'UTR	NM_002639.4	NP_002630.2	P36952	SPB5_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 5	187			V -> L (in dbSNP:rs2289520). {ECO:0000269|PubMed:8290962}.		cellular component movement (GO:0006928)|extracellular matrix organization (GO:0030198)|morphogenesis of an epithelium (GO:0002009)|negative regulation of endopeptidase activity (GO:0010951)|prostate gland morphogenesis (GO:0060512)|regulation of epithelial cell proliferation (GO:0050678)|regulation of proteolysis (GO:0030162)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase inhibitor activity (GO:0004867)			kidney(3)|large_intestine(2)|lung(5)|ovary(1)|prostate(1)	12						TCCTTTCAGAGTCAACAAGGT	0.413													G|||	1547	0.308906	0.6316	0.1527	5008	,	,		21022	0.2222		0.0785	False		,,,				2504	0.3098				p.V187L		Atlas-SNP	.											.	SERPINB5	35	.	0			c.G559C						PASS	.	G	LEU/VAL	2380,2026	613.1+/-392.1	647,1086,470	83.0	81.0	82.0		559	0.3	1.0	18	dbSNP_100	82	564,8036	154.0+/-208.3	20,524,3756	yes	missense	SERPINB5	NM_002639.4	32	667,1610,4226	CC,CG,GG		6.5581,45.9828,22.6357	benign	187/376	61160320	2944,10062	2203	4300	6503	SO:0001583	missense	5268	exon5			TTCAGAGTCAACA	U04313	CCDS32839.1	18q21.33	2014-02-18	2005-08-18		ENSG00000206075	ENSG00000206075		"""Serine (or cysteine) peptidase inhibitors"""	8949	protein-coding gene	gene with protein product	"""protease inhibitor 5 (maspin)"""	154790	"""serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 5"""	PI5		8290962, 7724531, 16720730, 24172014	Standard	NM_002639		Approved	maspin	uc002liz.4	P36952	OTTHUMG00000141307	ENST00000382771.4:c.559G>C	18.37:g.61160320G>C	ENSP00000372221:p.Val187Leu	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	75	4	0.0533333	NM_002639	B2R6Y4|Q6N0B4|Q8WW89	Missense_Mutation	SNP	ENST00000382771.4	37	CCDS32839.1	515	0.2358058608058608	311	0.6321138211382114	42	0.11602209944751381	111	0.19405594405594406	51	0.06728232189973615	G	4.710	0.131937	0.08981	0.540172	0.065581	ENSG00000206075	ENST00000382771	T	0.17370	2.28	6.05	0.338	0.15974	Serpin domain (3);	0.442462	0.22622	N	0.057688	T	0.00012	0.0000	N	0.11845	0.185	0.35936	P	0.16709399999999996	B;B	0.16603	0.006;0.018	B;B	0.14023	0.009;0.01	T	0.39542	-0.9609	9	0.06236	T	0.91	.	9.3317	0.38025	0.5586:0.0:0.4414:0.0	rs2289520;rs17071197;rs52826237;rs60369335;rs2289520	187;187	P36952;P36952-2	SPB5_HUMAN;.	L	187	ENSP00000372221:V187L	ENSP00000372221:V187L	V	+	1	0	SERPINB5	59311300	0.978000	0.34361	0.999000	0.59377	0.985000	0.73830	0.260000	0.18424	0.113000	0.18004	0.655000	0.94253	GTC	G|0.748;C|0.252	0.252	strong		0.413	SERPINB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280629.1	NM_002639	
ARHGAP12	94134	hgsc.bcm.edu	37	10	32141460	32141460	+	Silent	SNP	T	T	C	rs2799021	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr10:32141460T>C	ENST00000344936.2	-	6	1389	c.1155A>G	c.(1153-1155)gaA>gaG	p.E385E	ARHGAP12_ENST00000311380.4_Silent_p.E338E|ARHGAP12_ENST00000375245.4_Silent_p.E338E|ARHGAP12_ENST00000396144.4_Silent_p.E385E|ARHGAP12_ENST00000375250.5_Silent_p.E385E	NM_001270697.1|NM_018287.6	NP_001257626.1|NP_060757.4	Q8IWW6	RHG12_HUMAN	Rho GTPase activating protein 12	385	WW 2. {ECO:0000255|PROSITE- ProRule:PRU00224}.				morphogenesis of an epithelial sheet (GO:0002011)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)			NS(1)|breast(3)|endometrium(2)|kidney(1)|large_intestine(11)|lung(10)|skin(1)|urinary_tract(2)	31		Prostate(175;0.0199)				GCAATTCCCATTCTGACCGAG	0.333													T|||	1161	0.231829	0.0545	0.2954	5008	,	,		15238	0.4127		0.2048	False		,,,				2504	0.2679				p.E385E		Atlas-SNP	.											.	ARHGAP12	79	.	0			c.A1155G						PASS	.	T		371,4035	187.8+/-214.3	16,339,1848	100.0	99.0	99.0		1155	2.1	1.0	10	dbSNP_100	99	1826,6774	327.9+/-318.0	191,1444,2665	no	coding-synonymous	ARHGAP12	NM_018287.5		207,1783,4513	CC,CT,TT		21.2326,8.4203,16.8922		385/847	32141460	2197,10809	2203	4300	6503	SO:0001819	synonymous_variant	94134	exon6			TTCCCATTCTGAC	AY033594	CCDS7170.1, CCDS59214.1, CCDS59215.1, CCDS59216.1, CCDS73082.1	10p11.22	2013-01-10			ENSG00000165322	ENSG00000165322		"""Rho GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"""	16348	protein-coding gene	gene with protein product		610577				11854031	Standard	NM_001270695		Approved	FLJ20737, FLJ10971, FLJ21785	uc001ivz.2	Q8IWW6	OTTHUMG00000017911	ENST00000344936.2:c.1155A>G	10.37:g.32141460T>C		Somatic	254	0	0		WXS	Illumina HiSeq	Phase_I	238	11	0.0462185	NM_001270696	B1ANY0|B1ANY1|B1ANY2|Q504X1|Q86UB3|Q8IWW7|Q8N3L1|Q9NT76	Silent	SNP	ENST00000344936.2	37	CCDS7170.1	505	0.23122710622710624	28	0.056910569105691054	89	0.24585635359116023	219	0.38286713286713286	169	0.22295514511873352	T	9.049	0.991719	0.18966	0.084203	0.212326	ENSG00000165322	ENST00000454919	.	.	.	5.85	2.14	0.27477	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.38672	-0.9650	3	.	.	.	.	10.3205	0.43762	0.0:0.2537:0.0:0.7463	rs2799021;rs17572817;rs56514703;rs2799021	.	.	.	V	61	.	.	M	-	1	0	ARHGAP12	32181466	0.998000	0.40836	0.997000	0.53966	0.961000	0.63080	0.386000	0.20702	0.108000	0.17862	0.455000	0.32223	ATG	T|0.798;C|0.202	0.202	strong		0.333	ARHGAP12-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000047465.1		
KRT83	3889	hgsc.bcm.edu	37	12	52710309	52710309	+	Silent	SNP	G	G	A	rs2257286	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr12:52710309G>A	ENST00000293670.3	-	6	1046	c.984C>T	c.(982-984)aaC>aaT	p.N328N		NM_002282.3	NP_002273.3	P78385	KRT83_HUMAN	keratin 83	328	Coil 2.|Rod.				aging (GO:0007568)|epidermis development (GO:0008544)|hair cycle (GO:0042633)	extracellular space (GO:0005615)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)	p.N328N(1)		NS(1)|central_nervous_system(1)|endometrium(4)|large_intestine(4)|lung(9)|prostate(1)|skin(4)|stomach(7)|upper_aerodigestive_tract(1)	32	Myeloproliferative disorder(4;0.0484)|all_hematologic(5;0.088)			BRCA - Breast invasive adenocarcinoma(357;0.189)		GGTTCAGCTCGTTGATCTCCT	0.602													g|||	1882	0.375799	0.5008	0.317	5008	,	,		19119	0.1885		0.4095	False		,,,				2504	0.407				p.N328N	GBM(41;747 834 12702 24089 39393)|Esophageal Squamous(97;805 1414 12559 28198 31861)	Atlas-SNP	.											KRT83,NS,carcinoma,0,1	KRT83	64	1	1	Substitution - coding silent(1)	stomach(1)	c.C984T						PASS	.	G		2156,2250	582.3+/-385.5	551,1054,598	127.0	101.0	110.0		984	-1.3	1.0	12	dbSNP_100	110	3529,5067	514.6+/-378.4	722,2085,1491	no	coding-synonymous	KRT83	NM_002282.3		1273,3139,2089	AA,AG,GG		41.054,48.9333,43.724		328/494	52710309	5685,7317	2203	4298	6501	SO:0001819	synonymous_variant	3889	exon6			CAGCTCGTTGATC	X99141	CCDS8823.1	12q13.13	2013-06-20	2006-07-17	2006-07-17	ENSG00000170523	ENSG00000170523		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6460	protein-coding gene	gene with protein product	"""hard keratin type II"""	602765	"""keratin, hair, basic, 3"""	KRTHB3		9084137, 16831889	Standard	NM_002282		Approved	Hb-3	uc001saf.2	P78385	OTTHUMG00000169632	ENST00000293670.3:c.984C>T	12.37:g.52710309G>A		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	89	6	0.0674157	NM_002282	A1A4S9|B2RC21|Q6NT21|Q9NSB3	Silent	SNP	ENST00000293670.3	37	CCDS8823.1																																																																																			.	.	weak		0.602	KRT83-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405182.1	NM_002282	
SALL3	27164	hgsc.bcm.edu	37	18	76753768	76753768	+	Missense_Mutation	SNP	C	C	G	rs2447437	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr18:76753768C>G	ENST00000537592.2	+	2	1777	c.1777C>G	c.(1777-1779)Ctc>Gtc	p.L593V	SALL3_ENST00000575389.2_Missense_Mutation_p.L593V|SALL3_ENST00000536229.3_Missense_Mutation_p.L460V	NM_171999.3	NP_741996.2	Q9BXA9	SALL3_HUMAN	spalt-like transcription factor 3	593			L -> V (in dbSNP:rs2447437). {ECO:0000269|Ref.1}.		forelimb morphogenesis (GO:0035136)|hindlimb morphogenesis (GO:0035137)|negative regulation of smoothened signaling pathway (GO:0045879)|olfactory bulb interneuron development (GO:0021891)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.L593V(1)		NS(2)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(8)|lung(40)|ovary(4)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	74		Esophageal squamous(42;0.129)|Melanoma(33;0.16)|Prostate(75;0.167)		OV - Ovarian serous cystadenocarcinoma(15;4.69e-06)|BRCA - Breast invasive adenocarcinoma(31;0.0256)		CGGGCCGCCCCTCACTAAAGC	0.731													C|||	3973	0.793331	0.5825	0.8444	5008	,	,		9900	0.9226		0.8648	False		,,,				2504	0.8354				p.L593V		Atlas-SNP	.											SALL3,NS,carcinoma,0,1	SALL3	162	1	1	Substitution - Missense(1)	prostate(1)	c.C1777G						scavenged	.	C	VAL/LEU	2422,1000		875,672,164	3.0	4.0	4.0		1777	5.2	0.2	18	dbSNP_100	4	6372,926		2808,756,85	yes	missense	SALL3	NM_171999.2	32	3683,1428,249	GG,GC,CC		12.6884,29.2227,17.9664	benign	593/1301	76753768	8794,1926	1711	3649	5360	SO:0001583	missense	27164	exon2			CCGCCCCTCACTA	AJ007421	CCDS12013.1	18q23	2013-10-17	2013-10-17		ENSG00000256463	ENSG00000256463		"""Zinc fingers, C2H2-type"""	10527	protein-coding gene	gene with protein product		605079	"""sal (Drosophila)-like 3"", ""sal-like 3 (Drosophila)"""			10610715	Standard	NM_171999		Approved	ZNF796	uc002lmt.3	Q9BXA9	OTTHUMG00000132896	ENST00000537592.2:c.1777C>G	18.37:g.76753768C>G	ENSP00000441823:p.Leu593Val	Somatic	4	1	0.25		WXS	Illumina HiSeq	Phase_I	6	3	0.5	NM_171999	Q9UGH1	Missense_Mutation	SNP	ENST00000537592.2	37	CCDS12013.1	1724	0.7893772893772893	287	0.5833333333333334	299	0.8259668508287292	511	0.8933566433566433	627	0.8271767810026385	C	0.073	-1.197989	0.01594	0.707773	0.873116	ENSG00000256463	ENST00000537592;ENST00000536229;ENST00000543056	T	0.08984	3.03	5.2	5.2	0.72013	.	0.464067	0.17974	N	0.155779	T	0.00012	0.0000	L	0.35288	1.05	0.80722	P	0.0	B;B	0.15473	0.013;0.006	B;B	0.18561	0.022;0.002	T	0.36237	-0.9756	9	0.14656	T	0.56	-21.7235	10.231	0.43256	0.2471:0.6277:0.1252:0.0	rs2447437	325;593	F5GXY4;Q9BXA9	.;SALL3_HUMAN	V	593;593;325	ENSP00000441823:L593V	ENSP00000299466:L593V	L	+	1	0	SALL3	74854756	0.002000	0.14202	0.157000	0.22605	0.006000	0.05464	0.292000	0.19011	2.584000	0.87258	0.563000	0.77884	CTC	C|0.211;G|0.789	0.789	strong		0.731	SALL3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256397.1	NM_171999	
AGBL1	123624	hgsc.bcm.edu	37	15	86940622	86940622	+	Silent	SNP	T	T	C	rs4362360	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr15:86940622T>C	ENST00000441037.2	+	17	2357	c.2262T>C	c.(2260-2262)acT>acC	p.T754T	AGBL1_ENST00000389298.3_Silent_p.T485T|AGBL1_ENST00000421325.2_Silent_p.T754T	NM_152336.2	NP_689549.2	Q96MI9	CBPC4_HUMAN	ATP/GTP binding protein-like 1	754					C-terminal protein deglutamylation (GO:0035609)|protein side chain deglutamylation (GO:0035610)	cytoplasm (GO:0005737)	metallocarboxypeptidase activity (GO:0004181)|tubulin binding (GO:0015631)|zinc ion binding (GO:0008270)			NS(3)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|liver(2)|lung(28)|ovary(2)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	62						AGGTGATCACTGCTCGAGTTC	0.428													C|||	3727	0.744209	0.9735	0.6859	5008	,	,		18211	0.88		0.4284	False		,,,				2504	0.6605				p.T754T		Atlas-SNP	.											.	AGBL1	151	.	0			c.T2262C						PASS	.	C		3501,379		1588,325,27	113.0	108.0	110.0		2262	-11.0	0.5	15	dbSNP_111	110	3879,4395		891,2097,1149	yes	coding-synonymous	AGBL1	NM_152336.2		2479,2422,1176	CC,CT,TT		46.8818,9.768,39.2792		754/1067	86940622	7380,4774	1940	4137	6077	SO:0001819	synonymous_variant	123624	exon17			GATCACTGCTCGA	AK056872	CCDS58398.1	15q25.3	2014-06-23			ENSG00000166748	ENSG00000166748			26504	protein-coding gene	gene with protein product	"""cytosolic carboxypeptidase 4"""	615496				21074048, 24094747	Standard	NM_152336		Approved	FLJ32310, CCP4	uc002blz.1	Q96MI9	OTTHUMG00000149978	ENST00000441037.2:c.2262T>C	15.37:g.86940622T>C		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	84	4	0.047619	NM_152336	A1A4X5|A6NJH6|C9JHL5	Silent	SNP	ENST00000441037.2	37	CCDS58398.1																																																																																			T|0.292;C|0.708	0.708	strong		0.428	AGBL1-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000314929.5	NM_152336	
ARHGAP42	143872	hgsc.bcm.edu	37	11	100847069	100847069	+	Missense_Mutation	SNP	G	G	A	rs569336	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr11:100847069G>A	ENST00000298815.8	+	20	2140	c.2137G>A	c.(2137-2139)Gtt>Att	p.V713I	ARHGAP42_ENST00000524892.2_Missense_Mutation_p.V679I	NM_152432.2	NP_689645.2	A6NI28	RHG42_HUMAN	Rho GTPase activating protein 42	713	Ser-rich.			V -> I (in Ref. 3; BAB71456). {ECO:0000305}.	signal transduction (GO:0007165)	intracellular (GO:0005622)	GTPase activator activity (GO:0005096)			endometrium(3)|skin(2)	5						CCCAGGAGACGTTTCCCCACC	0.488													G|||	2485	0.496206	0.1505	0.5274	5008	,	,		21331	0.997		0.2883	False		,,,				2504	0.6391				p.V713I		Atlas-SNP	.											.	ARHGAP42	32	.	0			c.G2137A						PASS	.	G	ILE/VAL	307,1077		34,239,419	64.0	49.0	54.0		2137	2.4	0.0	11	dbSNP_83	54	987,2195		160,667,764	yes	missense	ARHGAP42	NM_152432.2	29	194,906,1183	AA,AG,GG		31.0182,22.1821,28.3399	benign	713/875	100847069	1294,3272	692	1591	2283	SO:0001583	missense	143872	exon20			GGAGACGTTTCCC			11q22.1	2012-04-19			ENSG00000165895	ENSG00000165895		"""Rho GTPase activating proteins"""	26545	protein-coding gene	gene with protein product		615936				18954304	Standard	NM_152432		Approved	FLJ32810, GRAF3	uc001pge.2	A6NI28	OTTHUMG00000167530	ENST00000298815.8:c.2137G>A	11.37:g.100847069G>A	ENSP00000298815:p.Val713Ile	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	120	5	0.0416667	NM_152432	Q96M56	Missense_Mutation	SNP	ENST00000298815.8	37		1052	0.4816849816849817	87	0.17682926829268292	168	0.46408839779005523	572	1.0	225	0.29683377308707126	G	3.367	-0.129186	0.06753	0.221821	0.310182	ENSG00000165895	ENST00000524892;ENST00000298815	T;T	0.06849	3.25;3.34	5.7	2.36	0.29203	.	.	.	.	.	T	0.00012	0.0000	L	0.34521	1.04	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.37753	-0.9692	8	0.33141	T	0.24	.	12.4883	0.55885	0.2148:0.0:0.7852:0.0	rs569336;rs52827090;rs58116702;rs569336	713	A6NI28	RHG42_HUMAN	I	679;713	ENSP00000431776:V679I;ENSP00000298815:V713I	ENSP00000298815:V713I	V	+	1	0	ARHGAP42	100352279	0.011000	0.17503	0.008000	0.14137	0.397000	0.30659	1.390000	0.34464	0.760000	0.33108	0.655000	0.94253	GTT	G|0.552;A|0.448	0.448	strong		0.488	ARHGAP42-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_152432	
PMP2	5375	hgsc.bcm.edu	37	8	82357112	82357112	+	Silent	SNP	T	T	C	rs2229015	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr8:82357112T>C	ENST00000256103.2	-	2	322	c.186A>G	c.(184-186)gaA>gaG	p.E62E	RP11-157I4.4_ENST00000524085.2_RNA|PMP2_ENST00000519260.1_Intron	NM_002677.3	NP_002668.1	P02689	MYP2_HUMAN	peripheral myelin protein 2	62					membrane organization (GO:0061024)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	cholesterol binding (GO:0015485)|fatty acid binding (GO:0005504)|transporter activity (GO:0005215)			endometrium(1)|kidney(1)|large_intestine(1)|lung(3)	6			Epithelial(68;0.186)			TGAAGGAGATTTCTGTATTTT	0.398													C|||	1760	0.351438	0.357	0.3285	5008	,	,		19779	0.748		0.1412	False		,,,				2504	0.1677				p.E62E		Atlas-SNP	.											.	PMP2	21	.	0			c.A186G						PASS	.	C		1469,2937	678.9+/-403.6	258,953,992	142.0	140.0	141.0		186	4.6	1.0	8	dbSNP_98	141	1449,7151	750.6+/-407.4	131,1187,2982	no	coding-synonymous	PMP2	NM_002677.3		389,2140,3974	CC,CT,TT		16.8488,33.3409,22.4358		62/133	82357112	2918,10088	2203	4300	6503	SO:0001819	synonymous_variant	5375	exon2			GGAGATTTCTGTA	X62167	CCDS6229.1	8q21.3-q22.1	2013-03-01			ENSG00000147588	ENSG00000147588		"""Fatty acid binding protein family"""	9117	protein-coding gene	gene with protein product		170715				1720307, 8288226	Standard	NM_002677		Approved	MP2, FABP8, M-FABP	uc003ycb.1	P02689	OTTHUMG00000164600	ENST00000256103.2:c.186A>G	8.37:g.82357112T>C		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	110	8	0.0727273	NM_002677	Q6FHL4	Silent	SNP	ENST00000256103.2	37	CCDS6229.1																																																																																			T|0.706;C|0.294	0.294	strong		0.398	PMP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379365.1	NM_002677	
RFT1	91869	hgsc.bcm.edu	37	3	53125922	53125922	+	Silent	SNP	T	T	C	rs11242	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr3:53125922T>C	ENST00000296292.3	-	13	1684	c.1623A>G	c.(1621-1623)acA>acG	p.T541T	RP11-894J14.5_ENST00000607203.1_Intron|RFT1_ENST00000394738.3_Silent_p.T502T	NM_052859.3	NP_443091.1	Q96AA3	RFT1_HUMAN	RFT1 homolog (S. cerevisiae)	541					carbohydrate transport (GO:0008643)|cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	integral component of membrane (GO:0016021)	lipid transporter activity (GO:0005319)			NS(1)|breast(1)|kidney(1)|lung(5)|skin(2)|urinary_tract(2)	12				BRCA - Breast invasive adenocarcinoma(193;6.98e-05)|Kidney(197;0.0017)|KIRC - Kidney renal clear cell carcinoma(197;0.00192)|OV - Ovarian serous cystadenocarcinoma(275;0.104)		CCTGAAGTCATGTCATTTTGT	0.552													C|||	2456	0.490415	0.174	0.585	5008	,	,		18681	0.746		0.5964	False		,,,				2504	0.4785				p.T541T		Atlas-SNP	.											RFT1,colon,carcinoma,-1,1	RFT1	34	1	0			c.A1623G						PASS	.	C		1123,3283	717.7+/-408.7	144,835,1224	119.0	98.0	105.0		1623	-11.1	0.0	3	dbSNP_52	105	4798,3802	538.1+/-383.3	1355,2088,857	no	coding-synonymous	RFT1	NM_052859.3		1499,2923,2081	CC,CT,TT		44.2093,25.488,45.5251		541/542	53125922	5921,7085	2203	4300	6503	SO:0001819	synonymous_variant	91869	exon13			AAGTCATGTCATT	AJ318099	CCDS2869.1	3p21.1	2014-02-06	2005-01-26		ENSG00000163933	ENSG00000163933			30220	protein-coding gene	gene with protein product	"""congenital disorder of glycosylation 1N"""	611908	"""RFT1, requiring fifty three 1 homolog (S. cerevisiae)"""			12477932	Standard	NM_052859		Approved	CDG1N	uc003dgj.3	Q96AA3	OTTHUMG00000074035	ENST00000296292.3:c.1623A>G	3.37:g.53125922T>C		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	129	6	0.0465116	NM_052859	Q96J03	Silent	SNP	ENST00000296292.3	37	CCDS2869.1																																																																																			T|0.505;C|0.495	0.495	strong		0.552	RFT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157136.2	NM_052859	
SLC7A13	157724	hgsc.bcm.edu	37	8	87229739	87229739	+	Missense_Mutation	SNP	C	C	T	rs4419794	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr8:87229739C>T	ENST00000297524.3	-	3	1242	c.1139G>A	c.(1138-1140)aGg>aAg	p.R380K	SLC7A13_ENST00000419776.2_Missense_Mutation_p.R371K|SLC7A13_ENST00000520624.1_5'Flank	NM_138817.2	NP_620172.2	Q8TCU3	S7A13_HUMAN	solute carrier family 7 (anionic amino acid transporter), member 13	380			R -> K (in dbSNP:rs4419794).			integral component of membrane (GO:0016021)	amino acid transmembrane transporter activity (GO:0015171)			breast(3)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(24)|ovary(1)|pancreas(1)|prostate(1)|skin(3)	45						GTATCTCCGCCTTAGTATTCC	0.299													C|||	973	0.194289	0.0401	0.1945	5008	,	,		17064	0.3383		0.1372	False		,,,				2504	0.3129				p.R380K		Atlas-SNP	.											SLC7A13,NS,carcinoma,+1,1	SLC7A13	97	1	0			c.G1139A						scavenged	.	C	LYS/ARG	248,4140		9,230,1955	29.0	34.0	32.0		1139	-0.8	0.0	8	dbSNP_111	32	1088,7496		80,928,3284	yes	missense	SLC7A13	NM_138817.2	26	89,1158,5239	TT,TC,CC		12.6747,5.6518,10.2991	benign	380/471	87229739	1336,11636	2194	4292	6486	SO:0001583	missense	157724	exon3			CTCCGCCTTAGTA	AJ417661	CCDS34917.1	8q21.3	2013-07-15	2011-07-12		ENSG00000164893	ENSG00000164893		"""Solute carriers"""	23092	protein-coding gene	gene with protein product						11907033, 11943479	Standard	XM_005250804		Approved	AGT-1, XAT2	uc003ydq.1	Q8TCU3	OTTHUMG00000163663	ENST00000297524.3:c.1139G>A	8.37:g.87229739C>T	ENSP00000297524:p.Arg380Lys	Somatic	322	1	0.00310559		WXS	Illumina HiSeq	Phase_I	332	12	0.0361446	NM_138817	Q05C37|Q08AH9|Q96N84	Missense_Mutation	SNP	ENST00000297524.3	37	CCDS34917.1	368	0.1684981684981685	18	0.036585365853658534	56	0.15469613259668508	193	0.3374125874125874	101	0.13324538258575197	C	0.005	-2.129682	0.00338	0.056518	0.126747	ENSG00000164893	ENST00000297524;ENST00000419776	D;D	0.88818	-2.43;-2.43	5.03	-0.761	0.11038	.	0.592368	0.15885	N	0.239861	T	0.00012	0.0000	N	0.00230	-1.795	0.80722	P	0.0	B;B	0.10296	0.003;0.0	B;B	0.01281	0.0;0.0	T	0.38478	-0.9659	9	0.27082	T	0.32	.	3.1871	0.06604	0.246:0.2762:0.0:0.4778	rs4419794;rs60737499;rs4419794	371;380	Q8TCU3-2;Q8TCU3	.;S7A13_HUMAN	K	380;371	ENSP00000297524:R380K;ENSP00000410982:R371K	ENSP00000297524:R380K	R	-	2	0	SLC7A13	87298855	0.931000	0.31567	0.005000	0.12908	0.003000	0.03518	0.841000	0.27613	0.109000	0.17891	-1.124000	0.02001	AGG	C|0.856;T|0.144	0.144	strong		0.299	SLC7A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374704.1	NM_138817	
TTN	7273	hgsc.bcm.edu	37	2	179454394	179454394	+	Silent	SNP	A	A	G	rs1560221	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr2:179454394A>G	ENST00000591111.1	-	254	57359	c.57135T>C	c.(57133-57135)taT>taC	p.Y19045Y	TTN-AS1_ENST00000590743.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN_ENST00000460472.2_Silent_p.Y11621Y|TTN-AS1_ENST00000419746.1_RNA|TTN_ENST00000589042.1_Silent_p.Y20686Y|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000589234.1_RNA|TTN_ENST00000342992.6_Silent_p.Y18118Y|TTN_ENST00000359218.5_Silent_p.Y11746Y|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN_ENST00000342175.6_Silent_p.Y11813Y|TTN-AS1_ENST00000590807.1_RNA			Q8WZ42	TITIN_HUMAN	titin	19045	Fibronectin type-III 38. {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)			GCCACTTTAGATAGACAAATG	0.448													G|||	2566	0.51238	0.5681	0.4092	5008	,	,		22023	0.7232		0.2545	False		,,,				2504	0.5583				p.Y20686Y		Atlas-SNP	.											.	TTN	18412	.	0			c.T62058C						PASS	.	G	,,,	2027,1825		546,935,445	194.0	187.0	189.0		34863,54354,35238,35439	3.9	1.0	2	dbSNP_88	189	1858,6404		196,1466,2469	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	,,,	742,2401,2914	GG,GA,AA		22.4885,47.378,32.0703	,,,	11621/26927,18118/33424,11746/27052,11813/27119	179454394	3885,8229	1926	4131	6057	SO:0001819	synonymous_variant	7273	exon304			CTTTAGATAGACA	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.57135T>C	2.37:g.179454394A>G		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	138	7	0.0507246	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																																																																																				A|0.558;G|0.442	0.442	strong		0.448	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
PRKG2	5593	hgsc.bcm.edu	37	4	82031675	82031675	+	Missense_Mutation	SNP	G	G	T			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr4:82031675G>T	ENST00000395578.1	-	15	1983	c.1867C>A	c.(1867-1869)Ctc>Atc	p.L623I	PRKG2_ENST00000545647.1_Missense_Mutation_p.L203I|PRKG2_ENST00000264399.1_Missense_Mutation_p.L623I|PRKG2_ENST00000418486.2_Missense_Mutation_p.L594I|PRKG2_ENST00000509169.1_5'UTR			Q13237	KGP2_HUMAN	protein kinase, cGMP-dependent, type II	623	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				blood coagulation (GO:0007596)|circadian regulation of gene expression (GO:0032922)|nitric oxide metabolic process (GO:0046209)|protein phosphorylation (GO:0006468)|regulation of nitric-oxide synthase activity (GO:0050999)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cGMP binding (GO:0030553)|cGMP-dependent protein kinase activity (GO:0004692)|protein kinase activity (GO:0004672)			NS(1)|breast(4)|central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(7)|lung(14)|ovary(1)|skin(2)	37						CCCTTGTTGAGAATGACTTCA	0.438																																					p.L623I		Atlas-SNP	.											.	PRKG2	195	.	0			c.C1867A						PASS	.						124.0	121.0	122.0					4																	82031675		2203	4300	6503	SO:0001583	missense	5593	exon14			TGTTGAGAATGAC	X94612	CCDS3589.1, CCDS75150.1	4q13.1-q21.1	2009-07-10			ENSG00000138669	ENSG00000138669	2.7.11.1		9416	protein-coding gene	gene with protein product		601591				7498513	Standard	XM_005263126		Approved	cGKII, PRKGR2	uc003hmh.2	Q13237	OTTHUMG00000130296	ENST00000395578.1:c.1867C>A	4.37:g.82031675G>T	ENSP00000378945:p.Leu623Ile	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	98	4	0.0408163	NM_006259	B4DMX3|E7EPE6|O00125|O60916	Missense_Mutation	SNP	ENST00000395578.1	37	CCDS3589.1	.	.	.	.	.	.	.	.	.	.	G	17.55	3.417180	0.62511	.	.	ENSG00000138669	ENST00000395578;ENST00000264399;ENST00000418486;ENST00000545647	T;T;T;T	0.67171	-0.25;-0.25;-0.25;-0.25	5.23	4.39	0.52855	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.060084	0.64402	D	0.000002	T	0.77731	0.4174	M	0.66297	2.02	0.58432	D	0.999998	D;D	0.76494	0.999;0.993	D;D	0.77004	0.984;0.989	T	0.78730	-0.2090	10	0.72032	D	0.01	-12.3911	9.7878	0.40686	0.1593:0.0:0.8407:0.0	.	594;623	E7EPE6;Q13237	.;KGP2_HUMAN	I	623;623;594;203	ENSP00000378945:L623I;ENSP00000264399:L623I;ENSP00000389038:L594I;ENSP00000439967:L203I	ENSP00000264399:L623I	L	-	1	0	PRKG2	82250699	1.000000	0.71417	1.000000	0.80357	0.923000	0.55619	2.122000	0.41987	1.211000	0.43351	0.557000	0.71058	CTC	.	.	none		0.438	PRKG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252639.1	NM_006259	
MUC6	4588	hgsc.bcm.edu	37	11	1016849	1016849	+	Missense_Mutation	SNP	C	C	G			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr11:1016849C>G	ENST00000421673.2	-	31	6002	c.5952G>C	c.(5950-5952)atG>atC	p.M1984I		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	1984	Thr-rich.				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)	p.M1984I(2)		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)		ATGTTGCAGTCATAGGACCTG	0.582																																					p.M1984I		Atlas-SNP	.											MUC6_ENST00000421673,NS,carcinoma,0,2	MUC6	408	2	2	Substitution - Missense(2)	lung(2)	c.G5952C						scavenged	.						1544.0	1533.0	1537.0					11																	1016849		2203	4298	6501	SO:0001583	missense	4588	exon31			TGCAGTCATAGGA	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.5952G>C	11.37:g.1016849C>G	ENSP00000406861:p.Met1984Ile	Somatic	679	21	0.0309278		WXS	Illumina HiSeq	Phase_I	771	30	0.0389105	NM_005961	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	Missense_Mutation	SNP	ENST00000421673.2	37	CCDS44513.1	.	.	.	.	.	.	.	.	.	.	c	0.326	-0.959077	0.02267	.	.	ENSG00000184956	ENST00000421673	T	0.17691	2.26	2.64	-5.29	0.02747	.	.	.	.	.	T	0.09598	0.0236	L	0.43152	1.355	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.27839	-1.0062	9	0.14656	T	0.56	.	1.5757	0.02624	0.1743:0.1847:0.3717:0.2692	.	1984	Q6W4X9	MUC6_HUMAN	I	1984	ENSP00000406861:M1984I	ENSP00000406861:M1984I	M	-	3	0	MUC6	1006849	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.496000	0.02291	-4.003000	0.00082	-2.547000	0.00178	ATG	.	.	none		0.582	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382120.2	XM_290540	
EPCAM	4072	hgsc.bcm.edu	37	2	47601106	47601106	+	Missense_Mutation	SNP	T	T	C	rs1126497|rs111849096	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr2:47601106T>C	ENST00000263735.4	+	3	702	c.344T>C	c.(343-345)aTg>aCg	p.M115T	EPCAM_ENST00000405271.1_Missense_Mutation_p.M143T	NM_002354.2	NP_002345.2	P16422	EPCAM_HUMAN	epithelial cell adhesion molecule	115	Thyroglobulin type-1. {ECO:0000255|PROSITE-ProRule:PRU00500}.		M -> T (in dbSNP:rs1126497). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:2108441, ECO:0000269|PubMed:2463074, ECO:0000269|PubMed:2469722}.		negative regulation of cell-cell adhesion mediated by cadherin (GO:2000048)|positive regulation of cell proliferation (GO:0008284)|positive regulation of stem cell proliferation (GO:2000648)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|signal transduction involved in regulation of gene expression (GO:0023019)|stem cell differentiation (GO:0048863)|ureteric bud development (GO:0001657)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	protein complex binding (GO:0032403)	p.0?(2)|p.?(1)		endometrium(3)|large_intestine(1)|liver(2)|lung(7)|skin(1)|stomach(1)	15						GGCACCTCCATGTGCTGGTGT	0.532													C|||	3336	0.666134	0.8888	0.5159	5008	,	,		17137	0.8323		0.4692	False		,,,				2504	0.5031				p.M115T		Atlas-SNP	.											.	EPCAM	27	.	3	Whole gene deletion(2)|Unknown(1)	haematopoietic_and_lymphoid_tissue(3)	c.T344C						PASS	.	C	THR/MET	3649,757	305.5+/-289.0	1530,589,84	74.0	69.0	70.0		344	1.7	0.4	2	dbSNP_86	70	3722,4878	618.5+/-396.8	801,2120,1379	yes	missense	EPCAM	NM_002354.2	81	2331,2709,1463	CC,CT,TT		43.2791,17.1811,43.3262	benign	115/315	47601106	7371,5635	2203	4300	6503	SO:0001583	missense	4072	exon3			CCTCCATGTGCTG	M33011	CCDS1833.1	2p21	2014-09-17	2008-12-16	2008-12-16	ENSG00000119888	ENSG00000119888		"""CD molecules"""	11529	protein-coding gene	gene with protein product		185535	"""antigen identified by monoclonal antibody AUA1"", ""tumor-associated calcium signal transducer 1"""	M4S1, MIC18, TACSTD1		8382772, 11306819	Standard	NM_002354		Approved	Ly74, TROP1, GA733-2, EGP34, EGP40, EGP-2, KSA, CD326, Ep-CAM, HEA125, KS1/4, MK-1, MH99, MOC31, 323/A3, 17-1A, TACST-1, CO-17A, ESA	uc002rvx.3	P16422	OTTHUMG00000128853	ENST00000263735.4:c.344T>C	2.37:g.47601106T>C	ENSP00000263735:p.Met115Thr	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	126	7	0.0555556	NM_002354	P18180|Q6FG26|Q6FG49|Q96C47|Q9UCD0	Missense_Mutation	SNP	ENST00000263735.4	37	CCDS1833.1	1440	0.6593406593406593	437	0.8882113821138211	182	0.5027624309392266	460	0.8041958041958042	361	0.4762532981530343	C	3.317	-0.139650	0.06669	0.828189	0.432791	ENSG00000119888	ENST00000405271;ENST00000263735;ENST00000419334	T;T;T	0.62105	0.05;0.05;0.05	5.93	1.71	0.24356	Thyroglobulin type-1 (6);	0.527053	0.22416	N	0.060350	T	0.00012	0.0000	N	0.01352	-0.895	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.44251	-0.9340	9	0.02654	T	1	-4.742	11.8944	0.52648	0.0:0.6732:0.0:0.3268	rs1126497;rs3181550;rs17845436;rs17858308;rs52820371;rs57528354;rs1126497	115;143	P16422;B5MCA4	EPCAM_HUMAN;.	T	143;115;191	ENSP00000385476:M143T;ENSP00000263735:M115T;ENSP00000389028:M191T	ENSP00000263735:M115T	M	+	2	0	EPCAM	47454610	0.325000	0.24660	0.371000	0.25978	0.878000	0.50629	0.040000	0.13905	0.160000	0.19432	-0.119000	0.15052	ATG	T|0.385;C|0.615	0.615	strong		0.532	EPCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250792.2		
NCKAP5	344148	hgsc.bcm.edu	37	2	133554288	133554288	+	Silent	SNP	A	A	G	rs1868076	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr2:133554288A>G	ENST00000409261.1	-	12	1195	c.822T>C	c.(820-822)cgT>cgC	p.R274R	NCKAP5_ENST00000405974.3_Silent_p.R274R|NCKAP5_ENST00000409213.1_Silent_p.R274R|NCKAP5_ENST00000317721.6_Silent_p.R274R	NM_207363.2	NP_997246.2	O14513	NCKP5_HUMAN	NCK-associated protein 5	274										NS(4)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(29)|lung(51)|prostate(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	118						GATCCAAGAGACGTGAGTGAA	0.408													G|||	3459	0.690695	0.7126	0.6729	5008	,	,		18207	0.8899		0.5398	False		,,,				2504	0.6237				p.R274R		Atlas-SNP	.											.	NCKAP5	322	.	0			c.T822C						PASS	.	G	,	2616,1088		925,766,161	63.0	60.0	61.0		822,822	0.1	0.0	2	dbSNP_92	61	4500,3706		1232,2036,835	no	coding-synonymous,coding-synonymous	NCKAP5	NM_207363.2,NM_207481.3	,	2157,2802,996	GG,GA,AA		45.1621,29.3737,40.2519	,	274/1910,274/591	133554288	7116,4794	1852	4103	5955	SO:0001819	synonymous_variant	344148	exon12			CAAGAGACGTGAG	AB005217	CCDS46417.1, CCDS46418.1	2q21.2	2010-02-17			ENSG00000176771	ENSG00000176771			29847	protein-coding gene	gene with protein product	"""Nck associated protein 5"", ""peripheral clock protein"""	608789				9344857	Standard	NM_207363		Approved	NAP5, ERIH1, ERIH2	uc002ttp.3	O14513	OTTHUMG00000153573	ENST00000409261.1:c.822T>C	2.37:g.133554288A>G		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	81	7	0.0864198	NM_207481	B8ZZL0|Q29SS9|Q29ST0|Q2NL90|Q6ZVE2|Q8NAS3	Silent	SNP	ENST00000409261.1	37	CCDS46418.1																																																																																			A|0.307;G|0.693	0.693	strong		0.408	NCKAP5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331663.1	NM_207481	
FSIP1	161835	hgsc.bcm.edu	37	15	39910404	39910404	+	Missense_Mutation	SNP	G	G	A	rs12908846	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr15:39910404G>A	ENST00000350221.3	-	11	1440	c.1231C>T	c.(1231-1233)Ctt>Ttt	p.L411F		NM_152597.4	NP_689810.3	Q8NA03	FSIP1_HUMAN	fibrous sheath interacting protein 1	411			L -> F (in dbSNP:rs12908846).							NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(4)|ovary(2)|skin(4)|stomach(2)|urinary_tract(1)	23		all_cancers(109;2.66e-19)|all_epithelial(112;2.66e-16)|Lung NSC(122;1.5e-11)|all_lung(180;4.03e-10)|Melanoma(134;0.0575)|Ovarian(310;0.0827)|Colorectal(260;0.119)		GBM - Glioblastoma multiforme(113;8.22e-06)|BRCA - Breast invasive adenocarcinoma(123;0.142)		TCATCCAGAAGACACTTTAAC	0.353													G|||	788	0.157348	0.0333	0.1196	5008	,	,		19671	0.2907		0.1471	False		,,,				2504	0.2249				p.L411F		Atlas-SNP	.											.	FSIP1	53	.	0			c.C1231T						PASS	.	G	PHE/LEU	230,4164		3,224,1970	51.0	54.0	53.0		1231	5.1	1.0	15	dbSNP_121	53	1107,7475		65,977,3249	yes	missense	FSIP1	NM_152597.4	22	68,1201,5219	AA,AG,GG		12.8991,5.2344,10.3036	probably-damaging	411/582	39910404	1337,11639	2197	4291	6488	SO:0001583	missense	161835	exon11			CCAGAAGACACTT	BC045191	CCDS10050.1	15q14	2012-11-19			ENSG00000150667	ENSG00000150667			21674	protein-coding gene	gene with protein product		615795				14702039	Standard	NM_152597		Approved	FLJ35989	uc001zki.3	Q8NA03	OTTHUMG00000172456	ENST00000350221.3:c.1231C>T	15.37:g.39910404G>A	ENSP00000280236:p.Leu411Phe	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	157	7	0.044586	NM_152597	Q6X2C8|Q86Y89	Missense_Mutation	SNP	ENST00000350221.3	37	CCDS10050.1	349	0.15979853479853479	16	0.032520325203252036	48	0.13259668508287292	178	0.3111888111888112	107	0.14116094986807387	G	20.4	3.987146	0.74589	0.052344	0.128991	ENSG00000150667	ENST00000350221	T	0.35789	1.29	5.06	5.06	0.68205	.	0.104654	0.38217	N	0.001773	T	0.00012	0.0000	L	0.29908	0.895	0.27465	P	0.9530472	D	0.89917	1.0	D	0.91635	0.999	T	0.18808	-1.0325	8	.	.	.	-7.7703	17.1261	0.86714	0.0:0.0:1.0:0.0	rs12908846;rs59692160;rs12908846	411	Q8NA03	FSIP1_HUMAN	F	411	ENSP00000280236:L411F	.	L	-	1	0	FSIP1	37697696	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.542000	0.67218	2.785000	0.95823	0.655000	0.94253	CTT	G|0.862;A|0.138	0.138	strong		0.353	FSIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252118.2	NM_152597	
NPR3	4883	hgsc.bcm.edu	37	5	32712111	32712111	+	Nonsense_Mutation	SNP	G	G	T			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr5:32712111G>T	ENST00000265074.8	+	1	572	c.229G>T	c.(229-231)Gag>Tag	p.E77*	NPR3_ENST00000415167.2_Nonsense_Mutation_p.E77*|NPR3_ENST00000434067.2_Intron|NPR3_ENST00000415685.2_Intron	NM_000908.3|NM_001204375.1	NP_000899.1|NP_001191304.1	P17342	ANPRC_HUMAN	natriuretic peptide receptor 3	77					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of smooth muscle cell proliferation (GO:0048662)|osteoclast proliferation (GO:0002158)|pancreatic juice secretion (GO:0030157)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of urine volume (GO:0035810)|regulation of blood pressure (GO:0008217)|regulation of osteoblast proliferation (GO:0033688)|skeletal system development (GO:0001501)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	G-protein coupled peptide receptor activity (GO:0008528)|hormone binding (GO:0042562)|natriuretic peptide receptor activity (GO:0016941)|peptide hormone binding (GO:0017046)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(12)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	24					Nesiritide(DB04899)	GCCGGCCATCGAGTATGCTCT	0.632																																					p.E77X		Atlas-SNP	.											NPR3,NS,carcinoma,-2,1	NPR3	65	1	0			c.G229T						scavenged	.						23.0	28.0	27.0					5																	32712111		1952	4151	6103	SO:0001587	stop_gained	4883	exon1			GCCATCGAGTATG		CCDS47196.1, CCDS56356.1, CCDS56357.1	5p13.3	2014-03-03	2014-03-03		ENSG00000113389	ENSG00000113389			7945	protein-coding gene	gene with protein product	"""guanylate cyclase C"""	108962	"""chromosome 5 open reading frame 23"", ""atrionatriuretic peptide receptor C"", ""natriuretic peptide receptor C/guanylate cyclase C (atrionatriuretic peptide receptor C)"", ""natriuretic peptide receptor C"""	NPRC, ANPRC, C5orf23		2162522, 1979052	Standard	NM_000908		Approved	GUCY2B, FLJ14054	uc003jhv.3	P17342	OTTHUMG00000150316	ENST00000265074.8:c.229G>T	5.37:g.32712111G>T	ENSP00000265074:p.Glu77*	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	95	2	0.0210526	NM_000908	A2RRD1|B4DT84|E7EPG9	Nonsense_Mutation	SNP	ENST00000265074.8	37	CCDS56357.1	.	.	.	.	.	.	.	.	.	.	G	40	7.958555	0.98583	.	.	ENSG00000113389	ENST00000265074;ENST00000415167	.	.	.	5.37	5.37	0.77165	.	0.244211	0.41605	D	0.000856	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.19147	T	0.46	-21.1844	18.7146	0.91671	0.0:0.0:1.0:0.0	.	.	.	.	X	77	.	ENSP00000265074:E77X	E	+	1	0	NPR3	32747868	1.000000	0.71417	1.000000	0.80357	0.799000	0.45148	3.766000	0.55280	2.539000	0.85634	0.561000	0.74099	GAG	.	.	none		0.632	NPR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317550.3	NM_000908	
ENPP4	22875	hgsc.bcm.edu	37	6	46108916	46108916	+	Silent	SNP	C	C	G	rs9472696	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr6:46108916C>G	ENST00000321037.4	+	3	1184	c.954C>G	c.(952-954)gcC>gcG	p.A318A		NM_014936.4	NP_055751.1	Q9Y6X5	ENPP4_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase 4 (putative)	318					blood coagulation (GO:0007596)|positive regulation of blood coagulation (GO:0030194)|purine ribonucleoside catabolic process (GO:0046130)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	bis(5'-adenosyl)-triphosphatase activity (GO:0047710)|metal ion binding (GO:0046872)			central_nervous_system(1)|large_intestine(2)|lung(7)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	18						TTTTGGTTGCCGATGAAGGCT	0.333													C|||	468	0.0934505	0.1339	0.0576	5008	,	,		17451	0.1716		0.0656	False		,,,				2504	0.0123				p.A318A		Atlas-SNP	.											.	ENPP4	44	.	0			c.C954G						PASS	.	C		607,3799	264.7+/-266.2	50,507,1646	92.0	83.0	86.0		954	-0.6	1.0	6	dbSNP_119	86	586,8008	155.4+/-209.4	15,556,3726	no	coding-synonymous	ENPP4	NM_014936.4		65,1063,5372	GG,GC,CC		6.8187,13.7767,9.1769		318/454	46108916	1193,11807	2203	4297	6500	SO:0001819	synonymous_variant	22875	exon3			GGTTGCCGATGAA	AB020686	CCDS34468.1	6p12.3	2010-06-24	2010-06-24		ENSG00000001561	ENSG00000001561			3359	protein-coding gene	gene with protein product						11027689	Standard	NM_014936		Approved	NPP4, KIAA0879	uc003oxy.3	Q9Y6X5	OTTHUMG00000014779	ENST00000321037.4:c.954C>G	6.37:g.46108916C>G		Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	160	7	0.04375	NM_014936	A8K5G1|Q7L2N1	Silent	SNP	ENST00000321037.4	37	CCDS34468.1																																																																																			C|0.901;G|0.099	0.099	strong		0.333	ENPP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040777.2		
HECTD4	283450	hgsc.bcm.edu	37	12	112654162	112654162	+	Missense_Mutation	SNP	C	C	T	rs372438469		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr12:112654162C>T	ENST00000430131.2	-	47	7278	c.6133G>A	c.(6133-6135)Gtg>Atg	p.V2045M	HECTD4_ENST00000550722.1_Missense_Mutation_p.V2321M|HECTD4_ENST00000377560.5_Missense_Mutation_p.V2295M			Q9Y4D8	HECD4_HUMAN	HECT domain containing E3 ubiquitin protein ligase 4	2045					glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)										TTATAGTGCACGGCTCGGCCG	0.507																																					p.V2333M		Atlas-SNP	.											C12orf51_ENST00000377560,colon,carcinoma,0,2	.	.	2	0			c.G6997A						scavenged	.	C	MET/VAL	0,3730		0,0,1865	23.0	24.0	24.0		6883	5.7	0.9	12		24	1,8127		0,1,4063	no	missense	C12orf51	NM_001109662.2	21	0,1,5928	TT,TC,CC		0.0123,0.0,0.0084	probably-damaging	2295/4247	112654162	1,11857	1865	4064	5929	SO:0001583	missense	283450	exon48			AGTGCACGGCTCG	AK091473		12q24.13	2013-07-17	2012-08-14	2012-08-14	ENSG00000173064	ENSG00000173064			26611	protein-coding gene	gene with protein product			"""chromosome 12 open reading frame 51"""	C12orf51		21270382	Standard	NM_001109662		Approved	FLJ34154, KIAA0614	uc021reb.1	Q9Y4D8	OTTHUMG00000150719	ENST00000430131.2:c.6133G>A	12.37:g.112654162C>T	ENSP00000404379:p.Val2045Met	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	131	3	0.0229008	NM_001109662	L8B0P6|Q3MJD5|Q6P0A0|Q7L530|Q8NB70|Q8WU73|Q96NT9|Q9NZS4|Q9UFT6	Missense_Mutation	SNP	ENST00000430131.2	37		.	.	.	.	.	.	.	.	.	.	C	17.98	3.521168	0.64747	0.0	1.23E-4	ENSG00000173064	ENST00000377560;ENST00000430131;ENST00000550722	T;T;T	0.56103	0.48;0.48;0.48	5.65	5.65	0.86999	.	.	.	.	.	T	0.41096	0.1144	N	0.14661	0.345	0.54753	D	0.999985	D	0.54047	0.964	B	0.41646	0.362	T	0.50065	-0.8871	9	0.87932	D	0	.	19.3194	0.94231	0.0:1.0:0.0:0.0	.	2045	Q9Y4D8	K0614_HUMAN	M	2295;2045;2321	ENSP00000366783:V2295M;ENSP00000404379:V2045M;ENSP00000449784:V2321M	ENSP00000366783:V2295M	V	-	1	0	C12orf51	111138545	1.000000	0.71417	0.917000	0.36280	0.032000	0.12392	7.434000	0.80377	2.659000	0.90383	0.655000	0.94253	GTG	.	.	weak		0.507	HECTD4-202	KNOWN	basic	protein_coding	protein_coding		NM_173813	
USH2A	7399	hgsc.bcm.edu	37	1	216420482	216420482	+	Missense_Mutation	SNP	G	G	T			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr1:216420482G>T	ENST00000307340.3	-	13	2640	c.2254C>A	c.(2254-2256)Cat>Aat	p.H752N	USH2A_ENST00000366943.2_Missense_Mutation_p.H752N|USH2A_ENST00000366942.3_Missense_Mutation_p.H752N	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	752	Laminin EGF-like 5. {ECO:0000255|PROSITE- ProRule:PRU00460}.				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)		ACTGAGCCATGGAGGTTACAC	0.413										HNSCC(13;0.011)																											p.H752N		Atlas-SNP	.											.	USH2A	1168	.	0			c.C2254A						PASS	.						105.0	108.0	107.0					1																	216420482		2203	4300	6503	SO:0001583	missense	7399	exon13			AGCCATGGAGGTT	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.2254C>A	1.37:g.216420482G>T	ENSP00000305941:p.His752Asn	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	154	33	0.214286	NM_007123	Q5VVM9|Q6S362|Q9NS27	Missense_Mutation	SNP	ENST00000307340.3	37	CCDS31025.1	.	.	.	.	.	.	.	.	.	.	G	12.25	1.880963	0.33255	.	.	ENSG00000042781	ENST00000307340;ENST00000366943;ENST00000366942	T;T;T	0.61742	0.08;0.08;0.08	5.89	1.43	0.22495	EGF-like, laminin (3);	0.310145	0.22620	N	0.057702	T	0.45696	0.1355	L	0.34521	1.04	0.28645	N	0.906962	B;P	0.42584	0.041;0.784	B;P	0.45753	0.04;0.492	T	0.33624	-0.9861	10	0.28530	T	0.3	.	6.7169	0.23308	0.2729:0.0:0.6066:0.1205	.	752;752	O75445-2;O75445	.;USH2A_HUMAN	N	752	ENSP00000305941:H752N;ENSP00000355910:H752N;ENSP00000355909:H752N	ENSP00000305941:H752N	H	-	1	0	USH2A	214487105	0.529000	0.26322	0.945000	0.38365	0.997000	0.91878	-0.016000	0.12613	0.393000	0.25203	0.655000	0.94253	CAT	.	.	none		0.413	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123	
MAGED2	10916	hgsc.bcm.edu	37	X	54838077	54838077	+	Silent	SNP	C	C	T	rs2071932	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chrX:54838077C>T	ENST00000375068.1	+	6	1214	c.981C>T	c.(979-981)tcC>tcT	p.S327S	MAGED2_ENST00000218439.4_Silent_p.S327S|MAGED2_ENST00000375053.2_Silent_p.S327S|MAGED2_ENST00000375058.1_Silent_p.S327S|SNORA11_ENST00000408789.1_RNA|MAGED2_ENST00000375062.4_Silent_p.S242S|MAGED2_ENST00000396224.1_Silent_p.S327S|MAGED2_ENST00000375060.1_Silent_p.S242S|MAGED2_ENST00000347546.4_Silent_p.S309S			Q9UNF1	MAGD2_HUMAN	melanoma antigen family D, 2	327	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.					membrane (GO:0016020)				breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(8)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	26						CAGGCTATTCCTTGGAGAAGG	0.502													C|||	1622	0.429669	0.2943	0.2997	3775	,	,		16373	0.4494		0.2992	False		,,,				2504	0.2771				p.S327S		Atlas-SNP	.											.	MAGED2	74	.	0			c.C981T						PASS	.	C	,,	1381,2454		205,769,202,658,369	57.0	47.0	50.0		981,981,981	0.8	1.0	X	dbSNP_96	50	2273,4455		253,1099,668,1076,1204	no	coding-synonymous,coding-synonymous,coding-synonymous	MAGED2	NM_014599.4,NM_177433.1,NM_201222.1	,,	458,1868,870,1734,1573	TT,TC,T,CC,C		33.7842,36.0104,34.5924	,,	327/607,327/607,327/607	54838077	3654,6909	2203	4300	6503	SO:0001819	synonymous_variant	10916	exon6			CTATTCCTTGGAG	AF128527	CCDS14362.1	Xp11.2	2008-08-01			ENSG00000102316	ENSG00000102316			16353	protein-coding gene	gene with protein product	"""hepatocellular carcinoma associated protein"", ""breast cancer associated gene 1"", ""melanoma-associated antigen D2"", ""hepatocellular carcinoma-associated protein HCA10"""	300470					Standard	NM_014599		Approved	JCL-1, BCG1, 11B6, MAGE-D2, HCA10, MAGED, MGC8386	uc004dtk.1	Q9UNF1	OTTHUMG00000021638	ENST00000375068.1:c.981C>T	X.37:g.54838077C>T		Somatic	247	0	0		WXS	Illumina HiSeq	Phase_I	217	10	0.046083	NM_201222	A6NMX0|O76058|Q5BJF3|Q8NAL6|Q9H218|Q9P0U9|Q9UM52	Silent	SNP	ENST00000375068.1	37	CCDS14362.1																																																																																			C|0.586;0|0.015	.	strong		0.502	MAGED2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056821.2	NM_014599	
LY75	4065	hgsc.bcm.edu	37	2	160737621	160737621	+	Silent	SNP	C	C	T	rs11675155	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr2:160737621C>T	ENST00000263636.4	-	8	1404	c.1377G>A	c.(1375-1377)acG>acA	p.T459T	LY75-CD302_ENST00000505052.1_Silent_p.T459T|LY75-CD302_ENST00000504764.1_Silent_p.T459T|LY75_ENST00000553424.1_Silent_p.T459T|LY75_ENST00000554112.1_Silent_p.T459T	NM_002349.3	NP_002340.2	O60449	LY75_HUMAN	lymphocyte antigen 75	459	C-type lectin 2. {ECO:0000255|PROSITE- ProRule:PRU00040}.				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)	p.T459T(1)		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)		CACAGTTGGGCGTCTTATTGT	0.368													C|||	1097	0.21905	0.1218	0.3746	5008	,	,		19539	0.3224		0.165	False		,,,				2504	0.1892				p.T459T		Atlas-SNP	.											LY75,NS,carcinoma,0,1	LY75	151	1	1	Substitution - coding silent(1)	prostate(1)	c.G1377A						PASS	.	C	,,	598,3808	264.1+/-265.8	45,508,1650	171.0	154.0	160.0		1377,1377,1377	-0.8	1.0	2	dbSNP_120	160	1508,7092	285.8+/-297.4	120,1268,2912	no	coding-synonymous,coding-synonymous,coding-synonymous	LY75,LY75-CD302	NM_001198759.1,NM_001198760.1,NM_002349.3	,,	165,1776,4562	TT,TC,CC		17.5349,13.5724,16.1925	,,	459/1874,459/1818,459/1723	160737621	2106,10900	2203	4300	6503	SO:0001819	synonymous_variant	4065	exon8			GTTGGGCGTCTTA	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.1377G>A	2.37:g.160737621C>T		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	98	4	0.0408163	NM_002349	O75913|Q53R46|Q53TF5|Q7Z575|Q7Z577	Silent	SNP	ENST00000263636.4	37	CCDS2211.1																																																																																			C|0.818;T|0.182	0.182	strong		0.368	LY75-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255035.1		
STARD13	90627	hgsc.bcm.edu	37	13	33703656	33703656	+	Silent	SNP	T	T	C	rs495680	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr13:33703656T>C	ENST00000336934.5	-	5	1274	c.1158A>G	c.(1156-1158)gaA>gaG	p.E386E	STARD13_ENST00000399365.3_Silent_p.E268E|STARD13_ENST00000255486.4_Silent_p.E378E	NM_001243476.1|NM_178006.3	NP_001230405.1|NP_821074.1	Q9Y3M8	STA13_HUMAN	StAR-related lipid transfer (START) domain containing 13	386					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|lipid particle (GO:0005811)|membrane (GO:0016020)|mitochondrion (GO:0005739)	GTPase activator activity (GO:0005096)|lipid binding (GO:0008289)			breast(2)|endometrium(2)|kidney(3)|large_intestine(6)|lung(18)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|soft_tissue(1)|upper_aerodigestive_tract(1)	40	all_epithelial(80;0.155)	Lung SC(185;0.0367)		all cancers(112;1.31e-05)|Epithelial(112;0.000142)|BRCA - Breast invasive adenocarcinoma(63;0.00936)|OV - Ovarian serous cystadenocarcinoma(117;0.0533)|Lung(94;0.143)|GBM - Glioblastoma multiforme(144;0.143)		GGGAGTGAAATTCATGCATAC	0.537													C|||	2582	0.515575	0.3275	0.621	5008	,	,		18928	0.5407		0.6103	False		,,,				2504	0.5716				p.E386E		Atlas-SNP	.											.	STARD13	100	.	0			c.A1158G						PASS	.	C	,,	1688,2718	651.8+/-399.3	303,1082,818	71.0	72.0	72.0		804,1158,1134	0.6	0.1	13	dbSNP_83	72	5395,3205	481.4+/-370.6	1717,1961,622	yes	coding-synonymous,coding-synonymous,coding-synonymous	STARD13	NM_052851.2,NM_178006.3,NM_178007.2	,,	2020,3043,1440	CC,CT,TT		37.2674,38.3114,45.5405	,,	268/996,386/1114,378/1106	33703656	7083,5923	2203	4300	6503	SO:0001819	synonymous_variant	90627	exon5			GTGAAATTCATGC	AL049801	CCDS9348.1, CCDS9349.1, CCDS9350.1	13q13.1	2013-08-13	2007-08-16		ENSG00000133121	ENSG00000133121		"""Rho GTPase activating proteins"", ""StAR-related lipid transfer (START) domain containing"""	19164	protein-coding gene	gene with protein product		609866	"""START domain containing 13"", ""long intergenic non-protein coding RNA 464"""	LINC00464		8812419	Standard	NM_178006		Approved	GT650, DLC2, ARHGAP37	uc001uuw.3	Q9Y3M8	OTTHUMG00000016708	ENST00000336934.5:c.1158A>G	13.37:g.33703656T>C		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	64	4	0.0625	NM_178006	A2A309|A2A310|Q5HYH1|Q5TAE3|Q6UN61|Q86TP6|Q86WQ3|Q86XT1	Silent	SNP	ENST00000336934.5	37	CCDS9348.1																																																																																			T|0.463;C|0.537	0.537	strong		0.537	STARD13-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276118.2	NM_001243466	
C12orf40	283461	hgsc.bcm.edu	37	12	40085906	40085906	+	Missense_Mutation	SNP	A	A	T	rs73270414	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr12:40085906A>T	ENST00000324616.5	+	11	1557	c.1403A>T	c.(1402-1404)aAg>aTg	p.K468M	C12orf40_ENST00000405531.3_Missense_Mutation_p.K468M	NM_001031748.2	NP_001026918.2	Q86WS4	CL040_HUMAN	chromosome 12 open reading frame 40	468										breast(4)|central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(14)|ovary(6)|prostate(1)|skin(2)	38						ATATCTACTAAGAAAATCTGT	0.244													A|||	650	0.129792	0.0658	0.098	5008	,	,		13634	0.1766		0.162	False		,,,				2504	0.1575				p.K468M		Atlas-SNP	.											C12orf40,fourth_ventricle,glioma,0,1	C12orf40	118	1	0			c.A1403T						scavenged	.	A	MET/LYS	277,3257		11,255,1501	28.0	26.0	27.0		1403	1.7	0.4	12	dbSNP_130	27	1306,6626		108,1090,2768	yes	missense	C12orf40	NM_001031748.2	95	119,1345,4269	TT,TA,AA		16.465,7.8381,13.806	benign	468/653	40085906	1583,9883	1767	3966	5733	SO:0001583	missense	283461	exon11			CTACTAAGAAAAT	AK097445	CCDS41770.1	12q12	2008-08-04			ENSG00000180116	ENSG00000180116			26846	protein-coding gene	gene with protein product						12477932	Standard	XM_005268806		Approved	FLJ40126	uc001rmc.3	Q86WS4	OTTHUMG00000133567	ENST00000324616.5:c.1403A>T	12.37:g.40085906A>T	ENSP00000317671:p.Lys468Met	Somatic	492	3	0.00609756		WXS	Illumina HiSeq	Phase_I	536	14	0.0261194	NM_001031748	B7WNU1|Q8IXY6|Q8N818|V9HW02	Missense_Mutation	SNP	ENST00000324616.5	37	CCDS41770.1	281	0.12866300366300365	29	0.05894308943089431	40	0.11049723756906077	97	0.16958041958041958	115	0.1517150395778364	A	4.175	0.031040	0.08101	0.078381	0.16465	ENSG00000180116	ENST00000405531;ENST00000324616	T;T	0.53206	0.63;0.72	2.84	1.66	0.24008	.	0.915548	0.09122	N	0.845588	T	0.00109	0.0003	N	0.24115	0.695	0.33319	P	0.432906	B	0.16603	0.018	B	0.20767	0.031	T	0.12760	-1.0535	9	0.38643	T	0.18	.	5.995	0.19489	0.7306:0.2694:0.0:0.0	.	468	Q86WS4	CL040_HUMAN	M	468	ENSP00000383897:K468M;ENSP00000317671:K468M	ENSP00000317671:K468M	K	+	2	0	C12orf40	38372173	0.046000	0.20272	0.429000	0.26710	0.178000	0.23041	0.308000	0.19314	0.475000	0.27415	0.379000	0.24179	AAG	A|0.858;T|0.142	0.142	strong		0.244	C12orf40-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257664.2	NM_173599	
VWA3A	146177	hgsc.bcm.edu	37	16	22144318	22144318	+	Missense_Mutation	SNP	C	C	T	rs1105929	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr16:22144318C>T	ENST00000389398.5	+	20	2066	c.1970C>T	c.(1969-1971)aCa>aTa	p.T657I	VWA3A_ENST00000389397.4_5'UTR	NM_173615.3	NP_775886.3	A6NCI4	VWA3A_HUMAN	von Willebrand factor A domain containing 3A	657	VWFA 1. {ECO:0000255|PROSITE- ProRule:PRU00219}.		T -> I (in dbSNP:rs1105929). {ECO:0000269|PubMed:14702039}.			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)		ATGGACACCACACCCCCTGCC	0.627													c|||	3000	0.599042	0.8177	0.353	5008	,	,		17039	0.7788		0.2734	False		,,,				2504	0.6278				p.T657I		Atlas-SNP	.											.	VWA3A	115	.	0			c.C1970T						PASS	.	T	ILE/THR	2900,1284		1007,886,199	45.0	50.0	48.0		1970	-5.8	0.0	16	dbSNP_86	48	2277,6105		321,1635,2235	yes	missense	VWA3A	NM_173615.3	89	1328,2521,2434	TT,TC,CC		27.1654,30.6883,41.1985	benign	657/1185	22144318	5177,7389	2092	4191	6283	SO:0001583	missense	146177	exon20			ACACCACACCCCC	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.1970C>T	16.37:g.22144318C>T	ENSP00000374049:p.Thr657Ile	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	71	5	0.0704225	NM_173615	A4QMU8|A6NNC0|Q6UTX4|Q6ZQZ9|Q8IUY6|Q8N9W1	Missense_Mutation	SNP	ENST00000389398.5	37	CCDS45441.1	1120	0.5128205128205128	370	0.7520325203252033	119	0.3287292817679558	422	0.7377622377622378	209	0.2757255936675462	c	0.412	-0.912760	0.02415	0.693117	0.271654	ENSG00000175267	ENST00000389398;ENST00000299840	T	0.23348	1.91	5.49	-5.8	0.02347	.	1.126930	0.06439	N	0.725536	T	0.00012	0.0000	N	0.03115	-0.41	0.80722	P	0.0	B;B	0.09022	0.002;0.001	B;B	0.14023	0.01;0.002	T	0.31888	-0.9927	9	0.15499	T	0.54	.	12.3394	0.55085	0.0:0.1593:0.1052:0.7355	rs1105929;rs4261529;rs52803518;rs59925558;rs1105929	657;281	A6NCI4;A6NCI4-2	VWA3A_HUMAN;.	I	657;280	ENSP00000374049:T657I	ENSP00000299840:T280I	T	+	2	0	VWA3A	22051819	0.000000	0.05858	0.000000	0.03702	0.209000	0.24338	-2.116000	0.01327	-1.309000	0.02315	-0.753000	0.03488	ACA	C|0.477;T|0.523	0.523	strong		0.627	VWA3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430052.1		
FARS2	10667	hgsc.bcm.edu	37	6	5431340	5431340	+	Missense_Mutation	SNP	A	A	G	rs11243011	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr6:5431340A>G	ENST00000324331.6	+	4	1175	c.839A>G	c.(838-840)aAc>aGc	p.N280S	FARS2_ENST00000274680.4_Missense_Mutation_p.N280S			O95363	SYFM_HUMAN	phenylalanyl-tRNA synthetase 2, mitochondrial	280			N -> S (in dbSNP:rs11243011). {ECO:0000269|PubMed:14702039, ECO:0000269|Ref.3, ECO:0000269|Ref.7}.		gene expression (GO:0010467)|phenylalanyl-tRNA aminoacylation (GO:0006432)|tRNA aminoacylation for protein translation (GO:0006418)|tRNA processing (GO:0008033)	mitochondrial matrix (GO:0005759)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|phenylalanine-tRNA ligase activity (GO:0004826)|tRNA binding (GO:0000049)	p.N280S(1)		endometrium(3)|kidney(1)|large_intestine(5)|lung(3)|prostate(1)|stomach(2)	15	Ovarian(93;0.11)	all_hematologic(90;0.0104)			L-Phenylalanine(DB00120)	ATGGAGATCAACTTTCATGGA	0.418													A|||	1178	0.235224	0.0552	0.2349	5008	,	,		19965	0.4772		0.161	False		,,,				2504	0.3057				p.N280S		Atlas-SNP	.											FARS2,NS,carcinoma,0,1	FARS2	33	1	1	Substitution - Missense(1)	stomach(1)	c.A839G						scavenged	.	A	SER/ASN	325,4081	171.9+/-202.1	8,309,1886	193.0	178.0	183.0		839	3.1	1.0	6	dbSNP_120	183	1654,6946	305.0+/-307.2	166,1322,2812	yes	missense	FARS2	NM_006567.3	46	174,1631,4698	GG,GA,AA		19.2326,7.3763,15.2161	benign	280/452	5431340	1979,11027	2203	4300	6503	SO:0001583	missense	10667	exon4			AGATCAACTTTCA	AF097441	CCDS4494.1	6p25.1	2011-07-01	2007-02-23	2004-12-03	ENSG00000145982	ENSG00000145982	6.1.1.20	"""Aminoacyl tRNA synthetases / Class II"""	21062	protein-coding gene	gene with protein product	"""phenylalanine tRNA ligase 2, mitochondrial"""	611592	"""phenylalanine-tRNA synthetase 1 (mitochondrial)"""	FARS1		10329163	Standard	NM_006567		Approved	dJ236A3.1	uc003mwr.2	O95363	OTTHUMG00000014178	ENST00000324331.6:c.839A>G	6.37:g.5431340A>G	ENSP00000316335:p.Asn280Ser	Somatic	161	1	0.00621118		WXS	Illumina HiSeq	Phase_I	151	8	0.0529801	NM_006567	B2R664|Q53F66|Q5TCS3|Q6FG29|Q9NPY7|Q9P062	Missense_Mutation	SNP	ENST00000324331.6	37	CCDS4494.1	473	0.21657509157509158	29	0.05894308943089431	78	0.2154696132596685	246	0.43006993006993005	120	0.158311345646438	A	10.50	1.366451	0.24771	0.073763	0.192326	ENSG00000145982	ENST00000274680;ENST00000397563;ENST00000324331;ENST00000445533	T;T;T	0.62639	0.01;0.01;0.01	5.5	3.13	0.36017	Aminoacyl-tRNA synthetase, class II (1);Phenylalanyl-tRNA synthetase (1);	0.385244	0.29932	N	0.010831	T	0.14184	0.0343	N	0.02916	-0.46	0.32635	P	0.5214190000000001	B	0.06786	0.001	B	0.04013	0.001	T	0.09100	-1.0690	9	0.17369	T	0.5	-15.1623	8.9638	0.35863	0.8529:0.0:0.1471:0.0	rs11243011;rs52836920;rs56643167;rs60399479;rs11243011	280	O95363	SYFM_HUMAN	S	280;130;280;76	ENSP00000274680:N280S;ENSP00000316335:N280S;ENSP00000392525:N76S	ENSP00000274680:N280S	N	+	2	0	FARS2	5376339	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	3.367000	0.52350	0.402000	0.25451	0.477000	0.44152	AAC	A|0.822;G|0.178	0.178	strong		0.418	FARS2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467790.1	NM_006567	
SP3	6670	hgsc.bcm.edu	37	2	174820750	174820750	+	Missense_Mutation	SNP	T	T	C	rs1047640	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr2:174820750T>C	ENST00000310015.6	-	4	1020	c.490A>G	c.(490-492)Aca>Gca	p.T164A	SP3_ENST00000418194.2_Missense_Mutation_p.T96A|SP3_ENST00000455789.2_Missense_Mutation_p.T111A|SP3_ENST00000483084.1_5'Flank	NM_001172712.1|NM_003111.4	NP_001166183.1|NP_003102.1	Q02447	SP3_HUMAN	Sp3 transcription factor	164	Transactivation domain (Gln-rich).		T -> A (in dbSNP:rs1047640). {ECO:0000269|PubMed:12297010, ECO:0000269|PubMed:1454515, ECO:0000269|PubMed:15474306}.		B cell differentiation (GO:0030183)|definitive hemopoiesis (GO:0060216)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic placenta development (GO:0001892)|embryonic process involved in female pregnancy (GO:0060136)|embryonic skeletal system development (GO:0048706)|enucleate erythrocyte differentiation (GO:0043353)|granulocyte differentiation (GO:0030851)|liver development (GO:0001889)|lung development (GO:0030324)|megakaryocyte differentiation (GO:0030219)|monocyte differentiation (GO:0030224)|natural killer cell differentiation (GO:0001779)|negative regulation of transcription, DNA-templated (GO:0045892)|ossification (GO:0001503)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|T cell differentiation (GO:0030217)|trophectodermal cell differentiation (GO:0001829)	nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|double-stranded DNA binding (GO:0003690)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)	p.T164A(1)	EWSR1/SP3(3)	NS(2)|large_intestine(3)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	9			OV - Ovarian serous cystadenocarcinoma(117;0.185)			CTGGACACTGTACCATTTGAT	0.428													T|||	645	0.128794	0.0061	0.0922	5008	,	,		20313	0.3413		0.1183	False		,,,				2504	0.1125				p.T164A		Atlas-SNP	.											SP3,NS,carcinoma,0,1	SP3	82	1	1	Substitution - Missense(1)	stomach(1)	c.A490G						PASS	.	T	ALA/THR,ALA/THR,ALA/THR	115,4291	89.2+/-127.9	0,115,2088	228.0	216.0	220.0		286,481,490	5.9	1.0	2	dbSNP_86	220	1029,7571	219.4+/-257.5	73,883,3344	yes	missense,missense,missense	SP3	NM_001017371.4,NM_001172712.1,NM_003111.4	58,58,58	73,998,5432	CC,CT,TT		11.9651,2.6101,8.7959	possibly-damaging,possibly-damaging,possibly-damaging	96/714,161/779,164/782	174820750	1144,11862	2203	4300	6503	SO:0001583	missense	6670	exon4			ACACTGTACCATT	M97191	CCDS2254.1, CCDS46452.1	2q31	2013-01-08			ENSG00000172845	ENSG00000172845		"""Specificity protein transcription factors"", ""Zinc fingers, C2H2-type"""	11208	protein-coding gene	gene with protein product		601804				1341900, 1454515	Standard	NM_003111		Approved	SPR-2	uc002uig.3	Q02447	OTTHUMG00000132333	ENST00000310015.6:c.490A>G	2.37:g.174820750T>C	ENSP00000310301:p.Thr164Ala	Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	158	7	0.0443038	NM_003111	A0AVL9|B4E2B7|Q69B26|Q69B27|Q8TD56|Q8WWU4|Q9BQR1	Missense_Mutation	SNP	ENST00000310015.6	37	CCDS2254.1	334	0.15293040293040294	4	0.008130081300813009	30	0.08287292817679558	201	0.3513986013986014	99	0.13060686015831136	T	9.922	1.212478	0.22289	0.026101	0.119651	ENSG00000172845	ENST00000310015;ENST00000455789;ENST00000418194	T;T;T	0.04454	3.62;3.64;3.65	5.95	5.95	0.96441	.	0.097447	0.64402	D	0.000001	T	0.00012	0.0000	L	0.36672	1.1	0.26350	P	0.9772296	B;B	0.06786	0.001;0.001	B;B	0.06405	0.002;0.002	T	0.45644	-0.9247	9	0.02654	T	1	.	16.4069	0.83677	0.0:0.0:0.0:1.0	rs1047640;rs3187647;rs3820899;rs16862215;rs52792192;rs59518808;rs1047640	164;111	Q02447;Q02447-6	SP3_HUMAN;.	A	164;111;96	ENSP00000310301:T164A;ENSP00000388903:T111A;ENSP00000406140:T96A	ENSP00000310301:T164A	T	-	1	0	SP3	174528996	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.075000	0.50073	2.272000	0.75746	0.460000	0.39030	ACA	T|0.878;C|0.122	0.122	strong		0.428	SP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255452.1	NM_003111	
PRDM16	63976	hgsc.bcm.edu	37	1	3301721	3301721	+	Silent	SNP	C	C	T	rs2282198	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr1:3301721C>T	ENST00000270722.5	+	4	493	c.444C>T	c.(442-444)tcC>tcT	p.S148S	PRDM16_ENST00000514189.1_Silent_p.S149S|PRDM16_ENST00000441472.2_Silent_p.S148S|PRDM16_ENST00000512462.1_3'UTR|PRDM16_ENST00000442529.2_Silent_p.S148S|PRDM16_ENST00000378398.3_Silent_p.S148S|PRDM16_ENST00000378391.2_Silent_p.S148S|PRDM16_ENST00000511072.1_Silent_p.S149S			Q9HAZ2	PRD16_HUMAN	PR domain containing 16	148	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				brown fat cell differentiation (GO:0050873)|negative regulation of granulocyte differentiation (GO:0030853)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neurogenesis (GO:0022008)|palate development (GO:0060021)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cellular respiration (GO:0043457)|somatic stem cell maintenance (GO:0035019)|tongue development (GO:0043586)|transcription, DNA-templated (GO:0006351)|white fat cell differentiation (GO:0050872)	nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|transcription coactivator activity (GO:0003713)			breast(4)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(7)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(3)	59	all_cancers(77;0.00208)|all_epithelial(69;0.000732)|Ovarian(185;0.0634)|Lung NSC(156;0.109)|all_lung(157;0.111)	all_epithelial(116;2.03e-21)|all_lung(118;7.55e-09)|Lung NSC(185;1.28e-06)|Breast(487;0.000792)|Renal(390;0.00137)|Hepatocellular(190;0.00515)|Myeloproliferative disorder(586;0.0267)|Ovarian(437;0.0365)|Lung SC(97;0.114)|Medulloblastoma(700;0.134)		Epithelial(90;5.59e-35)|OV - Ovarian serous cystadenocarcinoma(86;1.99e-20)|GBM - Glioblastoma multiforme(42;3.72e-11)|Colorectal(212;0.000425)|BRCA - Breast invasive adenocarcinoma(365;0.000946)|COAD - Colon adenocarcinoma(227;0.000968)|Kidney(185;0.00155)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0175)|Lung(427;0.137)		AGCAGATCTCCGAAGACCTGG	0.607			T	EVI1	"""MDS, AML"""								C|||	1705	0.340455	0.0386	0.3285	5008	,	,		18269	0.622		0.2684	False		,,,				2504	0.5409				p.S148S		Atlas-SNP	.		Dom	yes		1	1p36.23-p33	63976	PR domain containing 16		L	.	PRDM16	147	.	0			c.C444T						PASS	.	C	,	351,3947		22,307,1820	75.0	85.0	82.0		444,444	-9.1	0.5	1	dbSNP_100	82	2281,6267		290,1701,2283	no	coding-synonymous,coding-synonymous	PRDM16	NM_022114.3,NM_199454.2	,	312,2008,4103	TT,TC,CC		26.6846,8.1666,20.4889	,	148/1277,148/1258	3301721	2632,10214	2149	4274	6423	SO:0001819	synonymous_variant	63976	exon4			GATCTCCGAAGAC	AF294278	CCDS41236.1, CCDS44048.1, CCDS41236.2, CCDS44048.2	1p36.23-p33	2013-01-08			ENSG00000142611	ENSG00000142611		"""Zinc fingers, C2H2-type"""	14000	protein-coding gene	gene with protein product	"""MDS1/EVI1-like"", ""PR-domain zinc finger protein 16"", ""transcription factor MEL1"""	605557				11050005	Standard	NM_199454		Approved	MEL1, PFM13, KIAA1675, MGC166915	uc001akf.3	Q9HAZ2	OTTHUMG00000000581	ENST00000270722.5:c.444C>T	1.37:g.3301721C>T		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	88	4	0.0454545	NM_022114	A6NHQ8|B1AJP7|B1AJP8|B1AJP9|B1WB48|Q8WYJ9|Q9C0I8	Silent	SNP	ENST00000270722.5	37	CCDS41236.2																																																																																			C|0.713;T|0.287	0.287	strong		0.607	PRDM16-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000001382.3	NM_022114	
OR5D18	219438	hgsc.bcm.edu	37	11	55587457	55587457	+	Missense_Mutation	SNP	G	G	A	rs11231180	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr11:55587457G>A	ENST00000333976.4	+	1	372	c.352G>A	c.(352-354)Gtg>Atg	p.V118M		NM_001001952.1	NP_001001952.1	Q8NGL1	OR5DI_HUMAN	olfactory receptor, family 5, subfamily D, member 18	118			V -> M (in dbSNP:rs11231180).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.V118M(1)		NS(2)|breast(1)|endometrium(3)|large_intestine(6)|lung(33)|ovary(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	55		all_epithelial(135;0.208)				TTTATTAGCTGTGATGGCCTA	0.443													N|||	79	0.0157748	0.0	0.0	5008	,	,		18318	0.0754		0.0	False		,,,				2504	0.0031				p.V118M		Atlas-SNP	.											OR5D18,NS,carcinoma,0,1	OR5D18	121	1	1	Substitution - Missense(1)	stomach(1)	c.G352A						scavenged	.						161.0	159.0	160.0					11																	55587457		2200	4296	6496	SO:0001583	missense	219438	exon1			TTAGCTGTGATGG	AB065781	CCDS31510.1	11q11	2012-08-09			ENSG00000186119	ENSG00000186119		"""GPCR / Class A : Olfactory receptors"""	15285	protein-coding gene	gene with protein product							Standard	NM_001001952		Approved		uc010rin.2	Q8NGL1	OTTHUMG00000166811	ENST00000333976.4:c.352G>A	11.37:g.55587457G>A	ENSP00000335025:p.Val118Met	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	131	3	0.0229008	NM_001001952	Q6IF67|Q6IFD3|Q96RB3	Missense_Mutation	SNP	ENST00000333976.4	37	CCDS31510.1	42	0.019230769230769232	0	0.0	0	0.0	42	0.07342657342657342	0	0.0	.	12.55	1.970990	0.34754	.	.	ENSG00000186119	ENST00000333976	T	0.05855	3.38	4.84	3.85	0.44370	GPCR, rhodopsin-like superfamily (1);	0.000000	0.35739	N	0.003013	T	0.00815	0.0027	M	0.78344	2.41	0.19945	N	0.999941	P	0.41450	0.75	B	0.41723	0.365	T	0.04128	-1.0975	10	0.48119	T	0.1	-7.6736	13.0514	0.58957	0.0:0.0:0.8385:0.1614	rs11231180;rs11231180	118	Q8NGL1	OR5DI_HUMAN	M	118	ENSP00000335025:V118M	ENSP00000335025:V118M	V	+	1	0	OR5D18	55344033	0.011000	0.17503	0.831000	0.32960	0.812000	0.45895	0.640000	0.24705	2.458000	0.83093	0.560000	0.71715	GTG	G|0.974;A|0.026	0.026	strong		0.443	OR5D18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391515.1	NM_001001952	
PNRC1	10957	hgsc.bcm.edu	37	6	89793894	89793894	+	Silent	SNP	G	G	C	rs1130809	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr6:89793894G>C	ENST00000336032.3	+	2	1080	c.963G>C	c.(961-963)acG>acC	p.T321T	PNRC1_ENST00000369472.1_Silent_p.T136T|PNRC1_ENST00000354922.3_Silent_p.T136T	NM_006813.2	NP_006804.1	Q12796	PNRC1_HUMAN	proline-rich nuclear receptor coactivator 1	321					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				endometrium(1)|large_intestine(2)|lung(3)	6		all_cancers(76;3.64e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00527)		BRCA - Breast invasive adenocarcinoma(108;0.102)		ACTTAAAAACGCTCCTCAAAG	0.398										Multiple Myeloma(7;0.094)			G|||	1747	0.348842	0.2443	0.4006	5008	,	,		16481	0.6696		0.167	False		,,,				2504	0.3098				p.T321T		Atlas-SNP	.											.	PNRC1	17	.	0			c.G963C						PASS	.	G		989,3417	357.6+/-314.0	117,755,1331	58.0	57.0	57.0		963	3.4	1.0	6	dbSNP_86	57	1363,7235	255.9+/-280.6	110,1143,3046	no	coding-synonymous	PNRC1	NM_006813.2		227,1898,4377	CC,CG,GG		15.8525,22.4467,18.0867		321/328	89793894	2352,10652	2203	4299	6502	SO:0001819	synonymous_variant	10957	exon2			AAAAACGCTCCTC	U03105	CCDS5018.1	6q16.1	2008-02-05	2003-09-25	2003-09-26	ENSG00000146278	ENSG00000146278			17278	protein-coding gene	gene with protein product		606714	"""proline rich 2"""	PROL2		7578250	Standard	NM_006813		Approved	B4-2, PRR2	uc003pmv.3	Q12796	OTTHUMG00000015191	ENST00000336032.3:c.963G>C	6.37:g.89793894G>C		Somatic	263	0	0		WXS	Illumina HiSeq	Phase_I	174	7	0.0402299	NM_006813	B2R6Q0|E1P515|Q5T7J6|Q7Z5N0	Silent	SNP	ENST00000336032.3	37	CCDS5018.1																																																																																			G|0.746;C|0.254	0.254	strong		0.398	PNRC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041471.1	NM_006813	
SERPINA9	327657	hgsc.bcm.edu	37	14	94936107	94936107	+	Missense_Mutation	SNP	G	G	A	rs4905204	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr14:94936107G>A	ENST00000380365.3	-	2	149	c.71C>T	c.(70-72)gCc>gTc	p.A24V	SERPINA9_ENST00000546329.1_Intron|SERPINA9_ENST00000539349.1_5'UTR|SERPINA9_ENST00000337425.5_Missense_Mutation_p.A42V|SERPINA9_ENST00000298845.7_Missense_Mutation_p.A42V|SERPINA9_ENST00000424550.2_Intron|SERPINA9_ENST00000448305.2_Intron			Q86WD7	SPA9_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 9	24			A -> V (in dbSNP:rs4905204).		negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|membrane (GO:0016020)	serine-type endopeptidase inhibitor activity (GO:0004867)			NS(1)|central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(17)	21		all_cancers(154;0.0691)|all_epithelial(191;0.233)		Epithelial(152;0.144)|COAD - Colon adenocarcinoma(157;0.224)|all cancers(159;0.24)		GGGGGCATTGGCCGGGGACAC	0.527													G|||	364	0.0726837	0.0144	0.0331	5008	,	,		18408	0.1181		0.0755	False		,,,				2504	0.1299				p.A42V		Atlas-SNP	.											SERPINA9_ENST00000337425,NS,carcinoma,0,2	SERPINA9	105	2	0			c.C125T						scavenged	.	G	VAL/ALA,VAL/ALA	92,3928		1,90,1919	86.0	87.0	86.0		125,125	1.0	0.0	14	dbSNP_111	86	516,7828		19,478,3675	yes	missense,missense	SERPINA9	NM_001042518.1,NM_175739.3	64,64	20,568,5594	AA,AG,GG		6.1841,2.2886,4.9175	benign,benign	42/336,42/436	94936107	608,11756	2010	4172	6182	SO:0001583	missense	327657	exon2			GCATTGGCCGGGG	AY185497	CCDS41982.1, CCDS41983.1, CCDS61542.1	14q32.1	2014-02-18	2005-08-18		ENSG00000170054	ENSG00000170054		"""Serine (or cysteine) peptidase inhibitors"""	15995	protein-coding gene	gene with protein product		615677	"""serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 9"""			24172014	Standard	NM_175739		Approved	CENTERIN, SERPINA11b, GCET1	uc001ydf.3	Q86WD7	OTTHUMG00000167710	ENST00000380365.3:c.71C>T	14.37:g.94936107G>A	ENSP00000369723:p.Ala24Val	Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	158	5	0.0316456	NM_175739	B4DVH4|B9ZVX3|Q2T9J2|Q6UWP9|Q86WD4|Q86WD5|Q86WD6|Q86YP6|Q86YP7	Missense_Mutation	SNP	ENST00000380365.3	37		140	0.0641025641025641	9	0.018292682926829267	15	0.04143646408839779	67	0.11713286713286714	49	0.06464379947229551	G	3.440	-0.114198	0.06881	0.022886	0.061841	ENSG00000170054	ENST00000298845;ENST00000337425;ENST00000380365	D;D;D	0.87887	-2.31;-2.31;-2.31	3.99	0.963	0.19649	Serpin domain (1);	2.726190	0.02096	N	0.053529	T	0.03434	0.0099	N	0.08118	0	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.0;0.001;0.0	T	0.41324	-0.9515	9	0.33940	T	0.23	.	5.9522	0.19253	0.2665:0.0:0.5997:0.1338	rs4905204;rs52797710;rs4905204	24;42;42	Q86WD7;Q86WD7-7;Q86WD7-2	SPA9_HUMAN;.;.	V	42;42;24	ENSP00000298845:A42V;ENSP00000337133:A42V;ENSP00000369723:A24V	ENSP00000298845:A42V	A	-	2	0	SERPINA9	94005860	0.001000	0.12720	0.000000	0.03702	0.075000	0.17131	0.285000	0.18883	-0.298000	0.08921	-1.786000	0.00637	GCC	G|0.934;A|0.066	0.066	strong		0.527	SERPINA9-008	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000395803.2	NM_175739	
PTGFRN	5738	hgsc.bcm.edu	37	1	117491909	117491909	+	Missense_Mutation	SNP	C	C	T	rs560392261	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr1:117491909C>T	ENST00000393203.2	+	4	1075	c.928C>T	c.(928-930)Cgg>Tgg	p.R310W		NM_020440.2	NP_065173.2	Q9P2B2	FPRP_HUMAN	prostaglandin F2 receptor inhibitor	310	Ig-like C2-type 3.				lipid particle organization (GO:0034389)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				NS(1)|breast(1)|endometrium(4)|large_intestine(10)|liver(1)|lung(22)|ovary(1)|prostate(4)|stomach(1)|upper_aerodigestive_tract(1)	46	Lung SC(450;0.225)	all_cancers(81;0.00104)|all_lung(203;8.97e-05)|all_epithelial(167;0.000139)|Lung NSC(69;0.000446)		Lung(183;0.0704)|LUSC - Lung squamous cell carcinoma(189;0.227)|Colorectal(144;0.248)		CGATGACGTCCGGCCCGAGGT	0.597													C|||	2	0.000399361	0.0	0.0029	5008	,	,		18404	0.0		0.0	False		,,,				2504	0.0				p.R310W		Atlas-SNP	.											.	PTGFRN	91	.	0			c.C928T						PASS	.						115.0	99.0	105.0					1																	117491909		2203	4300	6503	SO:0001583	missense	5738	exon4			GACGTCCGGCCCG	AB014734	CCDS890.1	1p13.1	2013-01-29	2013-01-25		ENSG00000134247	ENSG00000134247		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9601	protein-coding gene	gene with protein product		601204	"""prostaglandin F2 receptor negative regulator"""			8655148	Standard	NM_020440		Approved	FPRP, EWI-F, CD9P-1, FLJ11001, KIAA1436, SMAP-6, CD315	uc001egv.1	Q9P2B2	OTTHUMG00000012028	ENST00000393203.2:c.928C>T	1.37:g.117491909C>T	ENSP00000376899:p.Arg310Trp	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	58	18	0.310345	NM_020440	Q5VVU9|Q8N2K6	Missense_Mutation	SNP	ENST00000393203.2	37	CCDS890.1	.	.	.	.	.	.	.	.	.	.	C	11.78	1.741688	0.30865	.	.	ENSG00000134247	ENST00000393203;ENST00000544471	T	0.65916	-0.18	5.77	2.78	0.32641	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.547984	0.19786	N	0.106117	T	0.43478	0.1249	L	0.27053	0.805	0.09310	N	1	D	0.89917	1.0	P	0.59703	0.862	T	0.28004	-1.0057	10	0.66056	D	0.02	-17.914	4.9405	0.13963	0.1512:0.6227:0.146:0.0801	.	310	Q9P2B2	FPRP_HUMAN	W	310;169	ENSP00000376899:R310W	ENSP00000376899:R310W	R	+	1	2	PTGFRN	117293432	0.445000	0.25657	0.005000	0.12908	0.012000	0.07955	2.573000	0.46007	0.781000	0.33589	-0.254000	0.11334	CGG	.	.	none		0.597	PTGFRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033271.1	NM_020440	
ASMTL	8623	hgsc.bcm.edu	37	X	1537953	1537953	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chrX:1537953C>T	ENST00000381317.3	-	10	1332	c.1300G>A	c.(1300-1302)Ggc>Agc	p.G434S	ASMTL_ENST00000381333.4_Missense_Mutation_p.G418S|ASMTL_ENST00000416733.2_Missense_Mutation_p.G358S|ASMTL_ENST00000534940.1_Missense_Mutation_p.G376S	NM_004192.3	NP_004183.2	O95671	ASML_HUMAN	acetylserotonin O-methyltransferase-like	434	ASMT-like.			G -> S (in Ref. 2; BAG63287). {ECO:0000305}.		cytoplasm (GO:0005737)	O-methyltransferase activity (GO:0008171)			NS(1)|breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(1)|lung(9)|pancreas(1)|soft_tissue(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)				TTCGTCATGCCGTGCATGGCC	0.672													c|||	600	0.119808	0.1256	0.1023	5008	,	,		15106	0.0972		0.1869	False		,,,				2504	0.0787				p.G434S		Atlas-SNP	.											.	ASMTL	56	.	0			c.G1300A						PASS	.		SER/GLY,SER/GLY,SER/GLY	596,3652		41,514,1569	37.0	50.0	46.0		1126,1252,1300	-3.8	0.0	X	dbSNP_134	46	1369,7073		125,1119,2977	no	missense,missense,missense	ASMTL	NM_001173473.1,NM_001173474.1,NM_004192.3	56,56,56	166,1633,4546	TT,TC,CC		16.2165,14.0301,15.4846	benign,benign,benign	376/564,418/606,434/622	1537953	1965,10725	2124	4221	6345	SO:0001583	missense	8623	exon10			TCATGCCGTGCAT	Y15521	CCDS43917.1, CCDS55362.1, CCDS55363.1	Xp22.3 and Yp11.3	2008-02-05			ENSG00000169093	ENSG00000169093		"""Pseudoautosomal regions / PAR1"""	751	protein-coding gene	gene with protein product		300162, 400011				9736779	Standard	NM_004192		Approved		uc004cpx.2	O95671	OTTHUMG00000021057	ENST00000381317.3:c.1300G>A	X.37:g.1537953C>T	ENSP00000370718:p.Gly434Ser	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	116	6	0.0517241	NM_004192	B4DX75|F5GXH4|J3JS33|Q5JQ53|Q8NBH5|Q96G02|Q9BUL6	Missense_Mutation	SNP	ENST00000381317.3	37	CCDS43917.1	309	0.14148351648351648	76	0.15447154471544716	37	0.10220994475138122	63	0.11013986013986014	133	0.17546174142480211	c	1.729	-0.494575	0.04322	0.140301	0.162165	ENSG00000169093	ENST00000416733;ENST00000534940;ENST00000381333;ENST00000381317	T;T;T;T	0.21031	2.03;2.03;2.03;2.03	1.88	-3.76	0.04359	O-methyltransferase, family 2 (1);	0.325338	0.30901	N	0.008641	T	0.00012	0.0000	N	0.13235	0.315	0.09310	N	1	B;B;B	0.14805	0.011;0.009;0.011	B;B;B	0.18871	0.023;0.011;0.019	T	0.26360	-1.0105	10	0.10636	T	0.68	.	3.4151	0.07373	0.264:0.2992:0.0:0.4368	.	358;418;434	E7ER97;O95671-2;O95671	.;.;ASML_HUMAN	S	358;376;418;434	ENSP00000410578:G358S;ENSP00000446410:G376S;ENSP00000370734:G418S;ENSP00000370718:G434S	ENSP00000370718:G434S	G	-	1	0	ASMTL	1497953	0.996000	0.38824	0.036000	0.18154	0.045000	0.14185	0.139000	0.16036	-1.731000	0.01360	-1.717000	0.00709	GGC	C|0.858;T|0.142	0.142	strong		0.672	ASMTL-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055595.1	NM_004192	
MUC21	394263	hgsc.bcm.edu	37	6	30954729	30954729	+	Missense_Mutation	SNP	G	G	C	rs111834205	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr6:30954729G>C	ENST00000376296.3	+	2	1018	c.777G>C	c.(775-777)gaG>gaC	p.E259D	MUC21_ENST00000486149.2_5'UTR	NM_001010909.2	NP_001010909.2	Q5SSG8	MUC21_HUMAN	mucin 21, cell surface associated	259	28 X 15 AA approximate tandem repeats.|Ser-rich.				cellular protein metabolic process (GO:0044267)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cell-substrate adhesion (GO:0010812)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(4)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(4)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	42						CCAACTCTGAGTCCAGCACGA	0.622																																					p.E259D		Atlas-SNP	.											MUC21,bladder,carcinoma,0,1	MUC21	98	1	0			c.G777C						scavenged	.						143.0	144.0	144.0					6																	30954729		2203	4300	6503	SO:0001583	missense	394263	exon2			CTCTGAGTCCAGC	AK056612	CCDS34388.1	6p21.33	2008-05-14	2008-05-14	2008-05-14	ENSG00000204544	ENSG00000204544		"""Mucins"""	21661	protein-coding gene	gene with protein product	"""epiglycanin"""		"""chromosome 6 open reading frame 205"""	C6orf205		17977904	Standard	NM_001010909		Approved	bCX31G15.2	uc003nsh.2	Q5SSG8	OTTHUMG00000031216	ENST00000376296.3:c.777G>C	6.37:g.30954729G>C	ENSP00000365473:p.Glu259Asp	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	126	5	0.0396825	NM_001010909	B0UZT7|B4DQ55|C9JMK2|D9N007|Q0VGF1|Q3B7T2|Q5SS94|Q6UXC5	Missense_Mutation	SNP	ENST00000376296.3	37	CCDS34388.1	128	0.05860805860805861	26	0.052845528455284556	42	0.11602209944751381	34	0.05944055944055944	26	0.03430079155672823	G	11.64	1.699361	0.30142	.	.	ENSG00000204544	ENST00000376296	T	0.01787	4.64	4.28	-5.78	0.02362	.	.	.	.	.	T	0.00412	0.0013	L	0.27053	0.805	0.09310	N	1	B	0.14438	0.01	B	0.11329	0.006	T	0.44726	-0.9309	8	.	.	.	.	6.5913	0.22647	0.2903:0.3922:0.3175:0.0	.	259	Q5SSG8	MUC21_HUMAN	D	259	ENSP00000365473:E259D	.	E	+	3	2	MUC21	31062708	0.000000	0.05858	0.000000	0.03702	0.039000	0.13416	-2.711000	0.00817	-0.718000	0.04949	-0.348000	0.07805	GAG	G|0.938;C|0.062	0.062	strong		0.622	MUC21-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000128579.3	NM_001010909	
CDH26	60437	hgsc.bcm.edu	37	20	58587641	58587641	+	Intron	SNP	C	C	T	rs375717739		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr20:58587641C>T	ENST00000244047.5	+	15	2483				CDH26_ENST00000244049.3_Silent_p.S77S|CDH26_ENST00000350849.6_Silent_p.S118S|CDH26_ENST00000497614.1_3'UTR|CDH26_ENST00000348616.4_Silent_p.S785S			Q8IXH8	CAD26_HUMAN	cadherin 26						homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(11)|lung(14)|ovary(4)|pancreas(2)|prostate(2)|skin(2)|urinary_tract(1)	44	all_lung(29;0.00963)		BRCA - Breast invasive adenocarcinoma(7;5.58e-09)			ACGTCTACAGCGAGGAAGGGG	0.547																																					p.S785S		Atlas-SNP	.											.	CDH26	229	.	0			c.C2355T						PASS	.	C	,	0,4406		0,0,2203	99.0	92.0	94.0		354,2355	-7.6	0.0	20		94	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	CDH26	NM_021810.4,NM_177980.2	,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,	118/166,785/833	58587641	1,13005	2203	4300	6503	SO:0001627	intron_variant	60437	exon18			CTACAGCGAGGAA	AF169690, AK055202	CCDS13485.1, CCDS13486.1	20q13.33	2010-01-26	2009-11-20		ENSG00000124215	ENSG00000124215		"""Cadherins / Major cadherins"""	15902	protein-coding gene	gene with protein product			"""cadherin-like 26"""				Standard	NM_177980		Approved	VR20	uc002ybe.3	Q8IXH8	OTTHUMG00000032874	ENST00000244047.5:c.2172+5799C>T	20.37:g.58587641C>T		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	78	24	0.307692	NM_177980	A2A2M5|B3KNX3|Q6P5Y6|Q8TCH3|Q9BQN4|Q9NRU1	Silent	SNP	ENST00000244047.5	37																																																																																				.	.	weak		0.547	CDH26-201	KNOWN	basic	protein_coding	protein_coding		NM_177980	
OR2T8	343172	hgsc.bcm.edu	37	1	248084440	248084440	+	Missense_Mutation	SNP	T	T	G	rs111379878	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr1:248084440T>G	ENST00000319968.4	+	1	121	c.121T>G	c.(121-123)Tcc>Gcc	p.S41A		NM_001005522.1	NP_001005522.1	A6NH00	OR2T8_HUMAN	olfactory receptor, family 2, subfamily T, member 8	41						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.S41A(1)		central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(20)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	34	all_cancers(71;0.000139)|all_epithelial(71;1.58e-05)|Breast(184;0.0117)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)	all_cancers(173;0.0211)	OV - Ovarian serous cystadenocarcinoma(106;0.0319)			GTTTGGCAATTCCCTCATGAT	0.502													T|||	184	0.0367412	0.059	0.0274	5008	,	,		14500	0.0109		0.0249	False		,,,				2504	0.0521				p.S41A		Atlas-SNP	.											OR2T8,NS,other,0,1	OR2T8	67	1	1	Substitution - Missense(1)	pancreas(1)	c.T121G						scavenged	.						63.0	57.0	59.0					1																	248084440		2202	4280	6482	SO:0001583	missense	343172	exon1			GGCAATTCCCTCA		CCDS31100.1	1q44	2012-08-09		2004-03-10	ENSG00000177462	ENSG00000177462		"""GPCR / Class A : Olfactory receptors"""	15020	protein-coding gene	gene with protein product				OR2T8P			Standard	XM_005273117		Approved		uc010pzc.2	A6NH00	OTTHUMG00000040205	ENST00000319968.4:c.121T>G	1.37:g.248084440T>G	ENSP00000326225:p.Ser41Ala	Somatic	479	4	0.00835073		WXS	Illumina HiSeq	Phase_I	597	7	0.0117253	NM_001005522		Missense_Mutation	SNP	ENST00000319968.4	37	CCDS31100.1	29	0.013278388278388278	20	0.04065040650406504	5	0.013812154696132596	0	0.0	4	0.005277044854881266	N	3.205	-0.162862	0.06502	.	.	ENSG00000177462	ENST00000319968	T	0.00012	9.33	3.65	-0.565	0.11771	GPCR, rhodopsin-like superfamily (1);	0.792834	0.10272	N	0.694616	T	0.00012	0.0000	N	0.10809	0.05	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.13953	-1.0490	10	0.06891	T	0.86	.	0.9955	0.01465	0.2883:0.2491:0.3226:0.14	.	41	A6NH00	OR2T8_HUMAN	A	41	ENSP00000326225:S41A	ENSP00000326225:S41A	S	+	1	0	OR2T8	246151063	0.000000	0.05858	0.060000	0.19600	0.299000	0.27559	-3.158000	0.00579	-0.030000	0.13804	-0.186000	0.12905	TCC	T|0.988;G|0.012	0.012	strong		0.502	OR2T8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096862.1	NM_001005522	
PRDM5	11107	hgsc.bcm.edu	37	4	121738049	121738049	+	Silent	SNP	T	T	C	rs343192	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr4:121738049T>C	ENST00000264808.3	-	6	921	c.681A>G	c.(679-681)ctA>ctG	p.L227L	PRDM5_ENST00000428209.2_Intron|PRDM5_ENST00000515109.1_Intron	NM_018699.2	NP_061169.2	Q9NQX1	PRDM5_HUMAN	PR domain containing 5	227					histone deacetylation (GO:0016575)|histone H3-K9 methylation (GO:0051567)|mitotic cell cycle (GO:0000278)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)|repressing transcription factor binding (GO:0070491)|sequence-specific DNA binding (GO:0043565)|transcription regulatory region DNA binding (GO:0044212)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(17)|pancreas(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	34						AAGACTCCTTTAGACTGCTTT	0.363													C|||	1377	0.27496	0.2057	0.3948	5008	,	,		17855	0.3562		0.3191	False		,,,				2504	0.1544				p.L227L		Atlas-SNP	.											PRDM5,NS,carcinoma,-2,1	PRDM5	76	1	0			c.A681G						scavenged	.	C		947,3459	735.3+/-410.7	106,735,1362	154.0	159.0	157.0		681	2.4	1.0	4	dbSNP_79	157	2711,5889	682.3+/-403.8	446,1819,2035	no	coding-synonymous	PRDM5	NM_018699.2		552,2554,3397	CC,CT,TT		31.5233,21.4934,28.1255		227/631	121738049	3658,9348	2203	4300	6503	SO:0001819	synonymous_variant	11107	exon6			CTCCTTTAGACTG	AF272897	CCDS3716.1, CCDS75187.1, CCDS75188.1	4q25-q26	2013-01-08			ENSG00000138738	ENSG00000138738		"""Zinc fingers, C2H2-type"""	9349	protein-coding gene	gene with protein product		614161					Standard	XM_005262706		Approved	PFM2	uc003idn.3	Q9NQX1	OTTHUMG00000132970	ENST00000264808.3:c.681A>G	4.37:g.121738049T>C		Somatic	353	0	0		WXS	Illumina HiSeq	Phase_I	306	11	0.0359477	NM_018699	Q0VAI9|Q0VAJ0|Q6NXQ7	Silent	SNP	ENST00000264808.3	37	CCDS3716.1																																																																																			T|0.707;C|0.293	0.293	strong		0.363	PRDM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256528.2		
MUC4	4585	hgsc.bcm.edu	37	3	195511131	195511131	+	Silent	SNP	C	C	T	rs71321826		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr3:195511131C>T	ENST00000463781.3	-	2	7779	c.7320G>A	c.(7318-7320)tcG>tcA	p.S2440S	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Silent_p.S2440S	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)		CTGTGGATGCCGAGGAAACGT	0.587																																					p.S2440S		Atlas-SNP	.											.	MUC4	1505	.	0			c.G7320A						PASS	.																																			SO:0001819	synonymous_variant	4585	exon2			GGATGCCGAGGAA	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.7320G>A	3.37:g.195511131C>T		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	89	7	0.0786517	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																																																																																			C|0.500;T|0.500	0.500	weak		0.587	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
WWP2	11060	hgsc.bcm.edu	37	16	69970329	69970329	+	Silent	SNP	A	A	G	rs1983016	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr16:69970329A>G	ENST00000359154.2	+	19	2192	c.2091A>G	c.(2089-2091)acA>acG	p.T697T	WWP2_ENST00000542271.1_Silent_p.T581T|WWP2_ENST00000568684.1_Silent_p.T258T|WWP2_ENST00000448661.1_Silent_p.T697T|WWP2_ENST00000544162.1_3'UTR|WWP2_ENST00000356003.2_Silent_p.T697T	NM_001270454.1|NM_007014.4	NP_001257383.1|NP_008945.2	O00308	WWP2_HUMAN	WW domain containing E3 ubiquitin protein ligase 2	697	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				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						TCCGGGTCACAGAGGAGAACA	0.592													g|||	4234	0.845447	0.907	0.7565	5008	,	,		18658	0.9663		0.7515	False		,,,				2504	0.7975				p.T697T		Atlas-SNP	.											WWP2,NS,carcinoma,0,2	WWP2	88	2	0			c.A2091G						scavenged	.		,	3794,602	265.0+/-266.4	1633,528,37	78.0	70.0	73.0		2091,774	-11.1	0.0	16	dbSNP_92	73	6405,2195	375.3+/-337.7	2394,1617,289	no	coding-synonymous,coding-synonymous	WWP2	NM_007014.3,NM_199424.1	,	4027,2145,326	GG,GA,AA		25.5233,13.6943,21.522	,	697/871,258/432	69970329	10199,2797	2198	4300	6498	SO:0001819	synonymous_variant	11060	exon19			GGTCACAGAGGAG	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.2091A>G	16.37:g.69970329A>G		Somatic	136	2	0.0147059		WXS	Illumina HiSeq	Phase_I	116	4	0.0344828	NM_001270454	A6NEP1|B2R706|B4DTL5|F5H213|H3BRF3|I3RSG8|Q6ZTQ5|Q96CZ2|Q9BWN6	Silent	SNP	ENST00000359154.2	37	CCDS10885.1																																																																																			A|0.193;G|0.807	0.807	strong		0.592	WWP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268954.1	NM_007014	
ATP6V1A	523	hgsc.bcm.edu	37	3	113517215	113517215	+	Silent	SNP	C	C	T			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr3:113517215C>T	ENST00000273398.3	+	12	1524	c.1416C>T	c.(1414-1416)ttC>ttT	p.F472F	ATP6V1A_ENST00000538620.1_Silent_p.F439F	NM_001690.3	NP_001681.2	P38606	VATA_HUMAN	ATPase, H+ transporting, lysosomal 70kDa, V1 subunit A	472					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)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|microvillus (GO:0005902)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|proton-transporting two-sector ATPase complex (GO:0016469)|proton-transporting V-type ATPase, V1 domain (GO:0033180)	ATP binding (GO:0005524)|proton-transporting ATPase activity, rotational mechanism (GO:0046961)	p.F472F(1)		breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(17)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34					Alendronate(DB00630)|Etidronic acid(DB01077)|Tiludronate(DB01133)	TCACAGAGTTCGTTCCTCTGA	0.438																																					p.F472F		Atlas-SNP	.											ATP6V1A,NS,carcinoma,0,2	ATP6V1A	71	2	1	Substitution - coding silent(1)	large_intestine(1)	c.C1416T						scavenged	.						148.0	137.0	141.0					3																	113517215		2203	4300	6503	SO:0001819	synonymous_variant	523	exon12			AGAGTTCGTTCCT	L09235	CCDS2976.1	3q13.31	2010-04-21	2002-08-29	2003-04-25	ENSG00000114573	ENSG00000114573	3.6.3.14	"""ATPases / V-type"""	851	protein-coding gene	gene with protein product		607027	"""ATPase, H+ transporting, lysosomal (vacuolar proton pump), alpha polypeptide, 70kD, isoform 1"""	VPP2, ATP6A1, ATP6V1A1		8463241	Standard	NM_001690		Approved	Vma1, VA68	uc003eao.3	P38606	OTTHUMG00000159295	ENST00000273398.3:c.1416C>T	3.37:g.113517215C>T		Somatic	225	2	0.00888889		WXS	Illumina HiSeq	Phase_I	201	7	0.0348259	NM_001690	B2RBR8|B7Z1R5|D3DN75|Q53YD9|Q96DY6|Q9UHY3	Silent	SNP	ENST00000273398.3	37	CCDS2976.1																																																																																			.	.	none		0.438	ATP6V1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354457.1	NM_001690	
SMPDL3A	10924	hgsc.bcm.edu	37	6	123126138	123126138	+	Silent	SNP	T	T	C	rs61741159	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr6:123126138T>C	ENST00000368440.4	+	6	1000	c.823T>C	c.(823-825)Ttg>Ctg	p.L275L	SMPDL3A_ENST00000539041.1_Silent_p.L144L	NM_006714.3	NP_006705.1	Q92484	ASM3A_HUMAN	sphingomyelin phosphodiesterase, acid-like 3A	275					sphingomyelin catabolic process (GO:0006685)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	hydrolase activity, acting on glycosyl bonds (GO:0016798)|sphingomyelin phosphodiesterase activity (GO:0004767)			breast(1)|cervix(1)|large_intestine(2)|lung(3)|ovary(1)|prostate(1)|urinary_tract(1)	10				GBM - Glioblastoma multiforme(226;0.236)		TAATGAGAAATTGATAGATAT	0.353													T|||	250	0.0499201	0.0303	0.1787	5008	,	,		15792	0.0456		0.003	False		,,,				2504	0.0378				p.L275L		Atlas-SNP	.											.	SMPDL3A	31	.	0			c.T823C						PASS	.	T		79,4327	68.7+/-106.4	0,79,2124	104.0	105.0	104.0		823	-2.2	0.2	6	dbSNP_129	104	31,8569	21.0+/-64.5	0,31,4269	yes	coding-synonymous	SMPDL3A	NM_006714.3		0,110,6393	CC,CT,TT		0.3605,1.793,0.8458		275/454	123126138	110,12896	2203	4300	6503	SO:0001819	synonymous_variant	10924	exon6			GAGAAATTGATAG	AK000184	CCDS5128.1, CCDS69190.1	6q22.32	2006-04-12			ENSG00000172594	ENSG00000172594			17389	protein-coding gene	gene with protein product	"""acid sphingomyelinase-like phosphodiesterase 3a"""	610728				12442002	Standard	XM_005266798		Approved	FLJ20177, ASM3A, ASML3a, yR36GH4.1	uc003pzg.3	Q92484	OTTHUMG00000015490	ENST00000368440.4:c.823T>C	6.37:g.123126138T>C		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	64	5	0.078125	NM_006714	B7Z729|Q8WV13	Silent	SNP	ENST00000368440.4	37	CCDS5128.1																																																																																			T|0.981;C|0.019	0.019	strong		0.353	SMPDL3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042039.1	NM_006714	
MECOM	2122	hgsc.bcm.edu	37	3	168810874	168810874	+	Silent	SNP	C	C	T	rs17466625	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr3:168810874C>T	ENST00000464456.1	-	12	3645	c.2445G>A	c.(2443-2445)tcG>tcA	p.S815S	MECOM_ENST00000433243.2_Silent_p.S825S|MECOM_ENST00000264674.3_Silent_p.S889S|MECOM_ENST00000468789.1_Silent_p.S824S|MECOM_ENST00000460814.1_Silent_p.S815S|MECOM_ENST00000392736.3_Silent_p.S824S|MECOM_ENST00000494292.1_Silent_p.S1003S|MECOM_ENST00000472280.1_Silent_p.S825S	NM_001164000.1	NP_001157472.1	Q13465	MDS1_HUMAN	MDS1 and EVI1 complex locus	0					regulation of transcription, DNA-templated (GO:0006355)		sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(13)|liver(1)|lung(28)|ovary(2)|pancreas(1)|prostate(2)|skin(12)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(4)	85						CAGAATGAGGCGACGATGTTG	0.393													C|||	455	0.0908546	0.0159	0.1037	5008	,	,		18533	0.0694		0.2008	False		,,,				2504	0.092				p.S1012S		Atlas-SNP	.											.	MECOM	216	.	0			c.G3036A						PASS	.	C	,,,,,,	206,4200	127.8+/-164.7	5,196,2002	111.0	100.0	104.0		2667,2472,2448,2445,2472,3036,2472	-1.1	1.0	3	dbSNP_123	104	1750,6850	317.2+/-313.1	180,1390,2730	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	MECOM	NM_001105077.3,NM_001105078.3,NM_001163999.1,NM_001164000.1,NM_001205194.1,NM_004991.3,NM_005241.3	,,,,,,	185,1586,4732	TT,TC,CC		20.3488,4.6754,15.0392	,,,,,,	889/1117,824/1052,816/1044,815/1043,824/1052,1012/1240,824/1052	168810874	1956,11050	2203	4300	6503	SO:0001819	synonymous_variant	2122	exon14			ATGAGGCGACGAT	S82592, AF164154	CCDS3205.1, CCDS54669.1, CCDS54670.1	3q26.2	2013-01-08	2009-08-07	2009-08-07	ENSG00000085276	ENSG00000085276		"""Zinc fingers, C2H2-type"""	3498	protein-coding gene	gene with protein product		165215	"""myelodysplasia syndrome 1"", ""ecotropic viral integration site 1"""	MDS1, EVI1		2115646, 8171026, 8643684	Standard	NM_001105077		Approved	MDS1-EVI1, PRDM3	uc011bpj.1	Q03112	OTTHUMG00000158596	ENST00000464456.1:c.2445G>A	3.37:g.168810874C>T		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	87	6	0.0689655	NM_004991	Q13466|Q6FH90	Silent	SNP	ENST00000464456.1	37	CCDS54669.1																																																																																			C|0.871;T|0.129	0.129	strong		0.393	MECOM-020	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000351519.1	NM_005241, NM_004991	
SLC24A5	283652	hgsc.bcm.edu	37	15	48426484	48426484	+	Missense_Mutation	SNP	A	A	G	rs1426654	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr15:48426484A>G	ENST00000341459.3	+	3	404	c.331A>G	c.(331-333)Aca>Gca	p.T111A	SLC24A5_ENST00000449382.2_Missense_Mutation_p.T51A	NM_205850.2	NP_995322.1	Q71RS6	NCKX5_HUMAN	solute carrier family 24 (sodium/potassium/calcium exchanger), member 5	111			T -> A (associated with SHEP4; greatly reduced exchange activity; dbSNP:rs1426654). {ECO:0000269|PubMed:16357253, ECO:0000269|PubMed:17999355}.		ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|negative regulation of melanin biosynthetic process (GO:0048022)|response to stimulus (GO:0050896)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	calcium, potassium:sodium antiporter activity (GO:0008273)|symporter activity (GO:0015293)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(17)|skin(1)|upper_aerodigestive_tract(1)	27		all_lung(180;0.00217)		all cancers(107;3.29e-10)|GBM - Glioblastoma multiforme(94;7.32e-07)		TGTTGCAGGCACAACTTTCAT	0.378													G|||	2816	0.5623	0.9259	0.4107	5008	,	,		20353	0.9881		0.003	False		,,,				2504	0.3149				p.T111A		Atlas-SNP	.											.	SLC24A5	64	.	0			c.A331G	GRCh37	CM054862	SLC24A5	M	rs1426654	PASS	.	G	ALA/THR	3388,1008	373.9+/-321.0	1323,742,133	156.0	163.0	161.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	331	5.6	1.0	15	dbSNP_88	161	42,8552	816.9+/-406.9	1,40,4256	yes	missense	SLC24A5	NM_205850.2	58	1324,782,4389	GG,GA,AA		0.4887,22.9299,26.4049	benign	111/501	48426484	3430,9560	2198	4297	6495	SO:0001583	missense	283652	exon3			GCAGGCACAACTT	AF348468	CCDS10128.1	15q21.1	2014-01-28	2013-07-18		ENSG00000188467	ENSG00000188467		"""Solute carriers"""	20611	protein-coding gene	gene with protein product	"""oculocutaneous albinism 6 (autosomal recessive)"""	609802	"""solute carrier family 24, member 5"""			23364476	Standard	XM_005254308		Approved	JSX, OCA6	uc001zwe.3	Q71RS6	OTTHUMG00000131494	ENST00000341459.3:c.331A>G	15.37:g.48426484A>G	ENSP00000341550:p.Thr111Ala	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	141	8	0.0567376	NM_205850	A5X8Z8|A5X8Z9|Q14CT4|Q6DKH3	Missense_Mutation	SNP	ENST00000341459.3	37	CCDS10128.1	1141	0.5224358974358975	454	0.9227642276422764	120	0.3314917127071823	564	0.986013986013986	3	0.00395778364116095	G	9.239	1.037742	0.19669	0.770701	0.004887	ENSG00000188467	ENST00000341459;ENST00000449382	T;T	0.61510	0.1;0.1	5.55	5.55	0.83447	Sodium/calcium exchanger membrane region (1);	0.000000	0.85682	N	0.000000	T	0.00012	0.0000	N	0.00007	-3.17	0.44908	P	0.0020719999999999628	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.44817	-0.9303	9	0.02654	T	1	.	14.8111	0.69996	0.0685:0.0:0.9315:0.0	rs1426654;rs52802038;rs58147390;rs1426654	51;111	A5X8Z9;Q71RS6	.;NCKX5_HUMAN	A	111;51	ENSP00000341550:T111A;ENSP00000389966:T51A	ENSP00000341550:T111A	T	+	1	0	SLC24A5	46213776	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.460000	0.80816	1.604000	0.50143	-0.186000	0.12905	ACA	A|0.618;G|0.382	0.382	strong		0.378	SLC24A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254340.2	NM_205850	
LILRB3	11025	hgsc.bcm.edu	37	19	54721049	54721049	+	Silent	SNP	A	A	G	rs60566950	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr19:54721049A>G	ENST00000391750.1	-	14	1945	c.1809T>C	c.(1807-1809)ctT>ctC	p.L603L	LILRB3_ENST00000469273.1_5'UTR|LILRA6_ENST00000419410.2_Silent_p.L604L|LILRB3_ENST00000407860.2_Silent_p.L620L|LILRA6_ENST00000440558.2_Silent_p.L603L|LILRA6_ENST00000270464.5_Silent_p.L604L|LILRA6_ENST00000391735.3_3'UTR|LILRB3_ENST00000346401.6_Silent_p.L615L|LILRB3_ENST00000424807.1_Silent_p.L603L|LILRB3_ENST00000245620.9_Silent_p.L604L			O75022	LIRB3_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 3	603					cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|immune system process (GO:0002376)|negative regulation of osteoclast differentiation (GO:0045671)	integral component of plasma membrane (GO:0005887)	receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			endometrium(3)|kidney(13)|large_intestine(1)|lung(6)|ovary(2)|prostate(5)|skin(2)|stomach(1)|urinary_tract(1)	34	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)		CCTTCCGTCTAAGGGTCAAGC	0.632													.|||	155	0.0309505	0.0998	0.0086	5008	,	,		17459	0.0		0.0	False		,,,				2504	0.0174				p.L604L		Atlas-SNP	.											LILRB3,NS,carcinoma,0,1	LILRB3	67	1	0			c.T1812C						scavenged	.	A	,	147,4257		24,99,2079	104.0	105.0	104.0		1812,1809	0.8	0.0	19	dbSNP_129	104	5,8595		0,5,4295	no	coding-synonymous,coding-synonymous	LILRB3	NM_001081450.1,NM_006864.2	,	24,104,6374	GG,GA,AA		0.0581,3.3379,1.1689	,	604/633,603/632	54721049	152,12852	2202	4300	6502	SO:0001819	synonymous_variant	11025	exon13			CCGTCTAAGGGTC	U91928	CCDS33105.1, CCDS46175.1	19q13.4	2013-01-11			ENSG00000204577	ENSG00000204577		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6607	protein-coding gene	gene with protein product		604820				9278324, 9382880	Standard	NM_006864		Approved	LIR-3, HL9, ILT5, LIR3, CD85a	uc002qee.1	O75022	OTTHUMG00000066626	ENST00000391750.1:c.1809T>C	19.37:g.54721049A>G		Somatic	137	1	0.00729927		WXS	Illumina HiSeq	Phase_I	174	5	0.0287356	NM_001081450	C9J1P3|C9JIP1|O15471|Q86U49	Silent	SNP	ENST00000391750.1	37	CCDS33105.1																																																																																			A|0.980;G|0.020	0.020	strong		0.632	LILRB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000142844.5	NM_006864	
AKAP2	11217	hgsc.bcm.edu	37	9	112900785	112900785	+	Silent	SNP	A	A	G	rs3739456	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr9:112900785A>G	ENST00000259318.7	+	2	2475	c.2268A>G	c.(2266-2268)tcA>tcG	p.S756S	AKAP2_ENST00000434623.2_Silent_p.S845S|PALM2-AKAP2_ENST00000374530.3_Silent_p.S987S|AKAP2_ENST00000482335.1_3'UTR|AKAP2_ENST00000510514.5_Silent_p.S987S|AKAP2_ENST00000555236.1_Silent_p.S987S|AKAP2_ENST00000374525.1_Silent_p.S845S|PALM2-AKAP2_ENST00000302798.7_Silent_p.S987S	NM_001136562.2	NP_001130034.1	Q9Y2D5	AKAP2_HUMAN	A kinase (PRKA) anchor protein 2	756										breast(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(16)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	33						ATGCCCCATCACTGCCCTCCA	0.522													G|||	1635	0.326478	0.1498	0.4107	5008	,	,		20700	0.6587		0.2575	False		,,,				2504	0.2342				p.S987S		Atlas-SNP	.											PALM2-AKAP2,NS,carcinoma,0,2	PALM2-AKAP2	117	2	0			c.A2961G						PASS	.	G	,,,,	738,3668	751.0+/-412.2	68,602,1533	71.0	66.0	68.0		2535,2268,2535,2961,2961	-6.5	0.4	9	dbSNP_107	68	2117,6483	707.9+/-405.6	258,1601,2441	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	AKAP2,PALM2-AKAP2	NM_001004065.4,NM_001136562.2,NM_001198656.1,NM_007203.4,NM_147150.2	,,,,	326,2203,3974	GG,GA,AA		24.6163,16.7499,21.9514	,,,,	845/949,756/860,845/962,987/1104,987/1091	112900785	2855,10151	2203	4300	6503	SO:0001819	synonymous_variant	445815	exon8			CCCATCACTGCCC	AB023137	CCDS43861.1, CCDS48003.1, CCDS56581.1	9q31.3	2009-10-16			ENSG00000241978	ENSG00000241978		"""A-kinase anchor proteins"""	372	protein-coding gene	gene with protein product	"""protein kinase A2"""	604582		PRKA2		10231032	Standard	NM_001136562		Approved	AKAP-KL, KIAA0920, DKFZp564L0716		Q9Y2D5	OTTHUMG00000156811	ENST00000259318.7:c.2268A>G	9.37:g.112900785A>G		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	48	5	0.104167	NM_007203	B1ALX9|B2RTU4|B3KQ00|B4DTZ2|B7ZW07|B9EJB5|Q9UG26	Silent	SNP	ENST00000259318.7	37	CCDS48003.1																																																																																			A|0.728;G|0.272	0.272	strong		0.522	AKAP2-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000346067.3	NM_001004065	
ZNF566	84924	hgsc.bcm.edu	37	19	36940698	36940698	+	Silent	SNP	A	A	G	rs10410711	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr19:36940698A>G	ENST00000434377.2	-	5	519	c.438T>C	c.(436-438)caT>caC	p.H146H	ZNF566_ENST00000454319.1_Silent_p.H147H|ZNF566_ENST00000424129.2_Silent_p.H146H|ZNF566_ENST00000493391.1_Silent_p.H42H|ZNF566_ENST00000392170.2_Silent_p.H147H	NM_032838.4	NP_116227.1	Q969W8	ZN566_HUMAN	zinc finger protein 566	146					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(2)|endometrium(3)|kidney(2)|large_intestine(2)|lung(12)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	24	Esophageal squamous(110;0.162)					GCAGATCTTCATGAGTGAATA	0.393													A|||	277	0.0553115	0.0772	0.0259	5008	,	,		18443	0.1151		0.0179	False		,,,				2504	0.0235				p.H147H		Atlas-SNP	.											.	ZNF566	40	.	0			c.T441C						PASS	.	A	,,,	254,4152	145.7+/-180.5	3,248,1952	160.0	158.0	159.0		441,438,438,438	-1.1	0.1	19	dbSNP_119	159	187,8413	84.0+/-146.5	1,185,4114	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ZNF566	NM_001145343.1,NM_001145344.1,NM_001145345.1,NM_032838.4	,,,	4,433,6066	GG,GA,AA		2.1744,5.7649,3.3907	,,,	147/420,146/419,146/419,146/419	36940698	441,12565	2203	4300	6503	SO:0001819	synonymous_variant	84924	exon5			ATCTTCATGAGTG	AK074497	CCDS12494.1, CCDS46061.1, CCDS74346.1	19q13.12	2013-01-08						"""Zinc fingers, C2H2-type"", ""-"""	25919	protein-coding gene	gene with protein product						12477932	Standard	NM_001145343		Approved	FLJ14779, MGC12515	uc010xtf.2	Q969W8		ENST00000434377.2:c.438T>C	19.37:g.36940698A>G		Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	179	9	0.0502793	NM_001145343	B7ZL95|Q2M3J1	Silent	SNP	ENST00000434377.2	37	CCDS12494.1																																																																																			A|0.947;G|0.053	0.053	strong		0.393	ZNF566-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000341054.1	NM_032838	
SHISA2	387914	hgsc.bcm.edu	37	13	26620777	26620777	+	Silent	SNP	G	G	A	rs77556088	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr13:26620777G>A	ENST00000319420.3	-	2	817	c.762C>T	c.(760-762)caC>caT	p.H254H		NM_001007538.1	NP_001007539.1	Q6UWI4	SHSA2_HUMAN	shisa family member 2	254					multicellular organismal development (GO:0007275)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(7)|ovary(1)|prostate(2)|skin(1)	17						GCACAGAGTCGTGCTGCACCG	0.572													A|||	555	0.110823	0.0825	0.0591	5008	,	,		20492	0.2351		0.0	False		,,,				2504	0.1718				p.H254H		Atlas-SNP	.											SHISA2,NS,carcinoma,0,3	SHISA2	43	3	0			c.C762T						PASS	.	A		268,4138	801.9+/-415.6	9,250,1944	138.0	111.0	120.0		762	-11.5	0.0	13	dbSNP_131	120	5,8595	819.0+/-406.8	0,5,4295	no	coding-synonymous	SHISA2	NM_001007538.1		9,255,6239	AA,AG,GG		0.0581,6.0826,2.099		254/296	26620777	273,12733	2203	4300	6503	SO:0001819	synonymous_variant	387914	exon2			AGAGTCGTGCTGC		CCDS31951.1	13q12.13	2013-07-31	2013-07-31	2008-04-01	ENSG00000180730	ENSG00000180730		"""Shisa homologs"""	20366	protein-coding gene	gene with protein product			"""chromosome 13 open reading frame 13"", ""transmembrane protein 46"", ""shisa homolog 2 (Xenopus laevis)"""	C13orf13, TMEM46			Standard	NM_001007538		Approved	bA398O19.2, PRO28631, WGAR9166, hShisa	uc001uqm.1	Q6UWI4	OTTHUMG00000016612	ENST00000319420.3:c.762C>T	13.37:g.26620777G>A		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	90	4	0.0444444	NM_001007538	B9EH70|Q5W0G8	Silent	SNP	ENST00000319420.3	37	CCDS31951.1																																																																																			G|0.962;A|0.038	0.038	strong		0.572	SHISA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044239.2	NM_001007538	
ARHGEF5	7984	hgsc.bcm.edu	37	7	144062632	144062632	+	Nonsense_Mutation	SNP	C	C	G	rs202036368		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr7:144062632C>G	ENST00000056217.5	+	2	3044	c.2870C>G	c.(2869-2871)tCa>tGa	p.S957*	ARHGEF5_ENST00000471847.2_5'Flank	NM_005435.3	NP_005426.2	Q12774	ARHG5_HUMAN	Rho guanine nucleotide exchange factor (GEF) 5	957					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)			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)					GCAGGGGTCTCAGAACACCCT	0.597																																					p.S957X		Atlas-SNP	.											ARHGEF5,NS,carcinoma,0,1	ARHGEF5	73	1	0			c.C2870G						scavenged	.						2.0	2.0	2.0					7																	144062632		723	1763	2486	SO:0001587	stop_gained	7984	exon2			GGGTCTCAGAACA	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.2870C>G	7.37:g.144062632C>G	ENSP00000056217:p.Ser957*	Somatic	127	30	0.23622		WXS	Illumina HiSeq	Phase_I	174	41	0.235632	NM_005435	A6NNJ2|Q6ZML7	Nonsense_Mutation	SNP	ENST00000056217.5	37	CCDS34771.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	37|37	6.577225|6.577225	0.97676|0.97676	.|.	.|.	ENSG00000050327|ENSG00000050327	ENST00000474817|ENST00000056217	.|.	.|.	.|.	4.06|4.06	2.22|2.22	0.28083|0.28083	.|.	.|0.258318	.|0.20430	.|N	.|0.092497	T|.	0.37237|.	0.0996|.	.|.	.|.	.|.	0.21020|0.21020	N|N	0.99981|0.99981	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.20940|.	-1.0260|.	4|.	.|0.48119	.|T	.|0.1	-0.0888|-0.0888	6.3968|6.3968	0.21616|0.21616	0.0:0.7685:0.0:0.2315|0.0:0.7685:0.0:0.2315	.|.	.|.	.|.	.|.	E|X	211|957	.|.	.|ENSP00000056217:S957X	Q|S	+|+	1|2	0|0	ARHGEF5|ARHGEF5	143693565|143693565	0.000000|0.000000	0.05858|0.05858	0.001000|0.001000	0.08648|0.08648	0.014000|0.014000	0.08584|0.08584	0.795000|0.795000	0.26972|0.26972	0.369000|0.369000	0.24510|0.24510	0.555000|0.555000	0.69702|0.69702	CAG|TCA	.	.	weak		0.597	ARHGEF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349981.1	NM_005435	
ZNF627	199692	hgsc.bcm.edu	37	19	11725413	11725413	+	Silent	SNP	G	G	A	rs12151212	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr19:11725413G>A	ENST00000361113.5	+	2	283	c.75G>A	c.(73-75)caG>caA	p.Q25Q	ZNF627_ENST00000588174.1_Silent_p.Q25Q	NM_145295.3	NP_660338.1	Q7L945	ZN627_HUMAN	zinc finger protein 627	25	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)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(6)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	14						ATCCTTCCCAGAAGAATCTCT	0.498													G|||	610	0.121805	0.0832	0.1167	5008	,	,		16866	0.0258		0.169	False		,,,				2504	0.228				p.Q25Q	Melanoma(112;173 1614 10731 17751 23322)	Atlas-SNP	.											ZNF627,NS,carcinoma,0,1	ZNF627	43	1	0			c.G75A						PASS	.	G		422,3984	203.8+/-226.2	17,388,1798	107.0	112.0	110.0		75	-0.9	0.5	19	dbSNP_120	110	1689,6911	306.1+/-307.8	164,1361,2775	no	coding-synonymous	ZNF627	NM_145295.3		181,1749,4573	AA,AG,GG		19.6395,9.5778,16.231		25/462	11725413	2111,10895	2203	4300	6503	SO:0001819	synonymous_variant	199692	exon2			TTCCCAGAAGAAT	AK074846	CCDS42502.1	19p13.2	2013-01-08				ENSG00000198551		"""Zinc fingers, C2H2-type"", ""-"""	30570	protein-coding gene	gene with protein product		612248				12477932	Standard	NM_145295		Approved	FLJ90365	uc002msk.2	Q7L945		ENST00000361113.5:c.75G>A	19.37:g.11725413G>A		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	107	6	0.0560748	NM_145295	O14846|Q4KMP9|Q6NT81|Q9BRG4	Silent	SNP	ENST00000361113.5	37	CCDS42502.1																																																																																			G|0.865;A|0.135	0.135	strong		0.498	ZNF627-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458875.1	NM_145295	
CPAMD8	27151	hgsc.bcm.edu	37	19	17108135	17108135	+	Missense_Mutation	SNP	C	C	T	rs3745340	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr19:17108135C>T	ENST00000443236.1	-	11	1053	c.1022G>A	c.(1021-1023)cGg>cAg	p.R341Q	CPAMD8_ENST00000388925.4_Missense_Mutation_p.R294Q	NM_015692.2	NP_056507.2	Q8IZJ3	CPMD8_HUMAN	C3 and PZP-like, alpha-2-macroglobulin domain containing 8	294						extracellular space (GO:0005615)|plasma membrane (GO:0005886)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(11)|central_nervous_system(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(17)|lung(14)|ovary(7)|pancreas(2)|prostate(4)|skin(5)	82						GTCGAAGTCCCGGGAGCCGAG	0.607													c|||	1649	0.329273	0.1649	0.353	5008	,	,		19240	0.5		0.3976	False		,,,				2504	0.2883				p.R341Q		Atlas-SNP	.											.	CPAMD8	192	.	0			c.G1022A						PASS	.	C	GLN/ARG	795,3235		79,637,1299	13.0	15.0	14.0		1022	-3.8	0.8	19	dbSNP_107	14	3138,5204		619,1900,1652	no	missense	CPAMD8	NM_015692.2	43	698,2537,2951	TT,TC,CC		37.6169,19.727,31.7895	possibly-damaging	341/1933	17108135	3933,8439	2015	4171	6186	SO:0001583	missense	27151	exon11			AAGTCCCGGGAGC	AY101765	CCDS42519.1	19p13.12	2008-02-05			ENSG00000160111	ENSG00000160111			23228	protein-coding gene	gene with protein product		608841				10574462	Standard	NM_015692		Approved	KIAA1283, VIP, K-CAP	uc002nfb.3	Q8IZJ3	OTTHUMG00000133549	ENST00000443236.1:c.1022G>A	19.37:g.17108135C>T	ENSP00000402505:p.Arg341Gln	Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	175	9	0.0514286	NM_015692	Q8NC09|Q9ULD7	Missense_Mutation	SNP	ENST00000443236.1	37	CCDS42519.1	815|815	0.3731684981684982|0.3731684981684982	87|87	0.17682926829268292|0.17682926829268292	147|147	0.40607734806629836|0.40607734806629836	276|276	0.4825174825174825|0.4825174825174825	305|305	0.4023746701846966|0.4023746701846966	c|c	9.619|9.619	1.133286|1.133286	0.21041|0.21041	0.19727|0.19727	0.376169|0.376169	ENSG00000160111|ENSG00000160111	ENST00000443236|ENST00000291440;ENST00000388925	.|T;T	.|0.51325	.|0.71;0.72	3.0|3.0	-3.79|-3.79	0.04320|0.04320	.|.	.|0.186387	.|0.32488	.|N	.|0.006027	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.00707|0.00707	-1.245|-1.245	0.51767|0.51767	P|P	6.799999999995698E-5|6.799999999995698E-5	.|B	.|0.06786	.|0.001	.|B	.|0.01281	.|0.0	T|T	0.47315|0.47315	-0.9127|-0.9127	4|9	.|0.25751	.|T	.|0.34	.|.	6.6288|6.6288	0.22845|0.22845	0.0:0.38:0.371:0.2489|0.0:0.38:0.371:0.2489	rs3745340;rs57931423;rs3745340|rs3745340;rs57931423;rs3745340	.|294	.|Q8IZJ3	.|CPMD8_HUMAN	R|Q	352|341;294	.|ENSP00000291440:R341Q;ENSP00000373577:R294Q	.|ENSP00000291440:R341Q	G|R	-|-	1|2	0|0	CPAMD8|CPAMD8	16969135|16969135	0.997000|0.997000	0.39634|0.39634	0.786000|0.786000	0.31890|0.31890	0.743000|0.743000	0.42351|0.42351	2.354000|2.354000	0.44098|0.44098	-0.514000|-0.514000	0.06488|0.06488	-0.417000|-0.417000	0.06048|0.06048	GGG|CGG	C|0.647;T|0.353	0.353	strong		0.607	CPAMD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257531.2	NM_015692	
DYNC1LI2	1783	hgsc.bcm.edu	37	16	66783159	66783159	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr16:66783159C>T	ENST00000258198.2	-	3	445	c.239G>A	c.(238-240)gGc>gAc	p.G80D	DYNC1LI2_ENST00000440564.2_Intron|RP11-61A14.4_ENST00000501143.1_lincRNA|DYNC1LI2_ENST00000443351.2_Missense_Mutation_p.G80D|DYNC1LI2_ENST00000379482.2_Missense_Mutation_p.G80D	NM_006141.2	NP_006132.1	O43237	DC1L2_HUMAN	dynein, cytoplasmic 1, light intermediate chain 2	80					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|centrosome localization (GO:0051642)|microtubule cytoskeleton organization (GO:0000226)|microtubule-based movement (GO:0007018)|transport (GO:0006810)	centrosome (GO:0005813)|cytoplasmic dynein complex (GO:0005868)|cytosol (GO:0005829)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			central_nervous_system(3)|endometrium(1)|large_intestine(3)|lung(2)|ovary(1)|skin(4)|stomach(1)	15		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0907)|Epithelial(162;0.212)		TCCTTTTTTGCCATGCTCAGC	0.458																																					p.G80D		Atlas-SNP	.											.	DYNC1LI2	37	.	0			c.G239A						PASS	.						246.0	213.0	224.0					16																	66783159		2200	4300	6500	SO:0001583	missense	1783	exon3			TTTTTGCCATGCT	AF035812	CCDS10818.1, CCDS67049.1	16q22.1	2008-02-05	2005-11-25	2005-11-25	ENSG00000135720	ENSG00000135720		"""Cytoplasmic dyneins"""	2966	protein-coding gene	gene with protein product		611406	"""dynein, cytoplasmic, light intermediate polypeptide 2"""	DNCLI2		16260502	Standard	NM_006141		Approved		uc002eqb.1	O43237	OTTHUMG00000137523	ENST00000258198.2:c.239G>A	16.37:g.66783159C>T	ENSP00000258198:p.Gly80Asp	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	88	4	0.0454545	NM_006141	A8K6V1|B4DZP4|Q8TAT3	Missense_Mutation	SNP	ENST00000258198.2	37	CCDS10818.1	.	.	.	.	.	.	.	.	.	.	C	13.91	2.377507	0.42105	.	.	ENSG00000135720	ENST00000258198;ENST00000379482;ENST00000443351	T;T;T	0.28666	1.6;1.6;1.6	4.81	4.81	0.61882	.	0.164538	0.56097	D	0.000039	T	0.13286	0.0322	N	0.03608	-0.345	0.39621	D	0.97003	B;B;B	0.23735	0.0;0.09;0.022	B;B;B	0.29440	0.004;0.01;0.102	T	0.13442	-1.0509	10	0.07175	T	0.84	-23.9298	11.5313	0.50612	0.0:0.9183:0.0:0.0816	.	80;80;80	B4DHD8;B4DZP4;O43237	.;.;DC1L2_HUMAN	D	80	ENSP00000258198:G80D;ENSP00000368795:G80D;ENSP00000394289:G80D	ENSP00000258198:G80D	G	-	2	0	DYNC1LI2	65340660	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.649000	0.54417	2.494000	0.84150	0.455000	0.32223	GGC	.	.	none		0.458	DYNC1LI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268846.1	NM_006141	
OR4N4	283694	hgsc.bcm.edu	37	15	22383189	22383189	+	Silent	SNP	G	G	A	rs1820851	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr15:22383189G>A	ENST00000328795.4	+	1	808	c.717G>A	c.(715-717)acG>acA	p.T239T	RP11-69H14.6_ENST00000558896.1_RNA	NM_001005241.2	NP_001005241.2	Q8N0Y3	OR4N4_HUMAN	olfactory receptor, family 4, subfamily N, member 4	239			T -> M (in dbSNP:rs475947). {ECO:0000269|Ref.1}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.T239T(2)		breast(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(19)|ovary(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	40		all_cancers(20;1.94e-20)|all_epithelial(15;3.94e-18)|Lung NSC(15;8.53e-15)|all_lung(15;2.87e-14)|Breast(32;0.00519)|Colorectal(260;0.101)	GBM - Glioblastoma multiforme(6;0.124)	all cancers(64;1.64e-11)|Epithelial(43;5.81e-10)|BRCA - Breast invasive adenocarcinoma(123;0.000255)|Kidney(6;0.00736)|KIRC - Kidney renal clear cell carcinoma(6;0.0135)|GBM - Glioblastoma multiforme(186;0.0963)		CCATGTCCACGTGCACCACTC	0.493																																					p.T239T		Atlas-SNP	.											OR4N4,NS,carcinoma,0,2	OR4N4	108	2	2	Substitution - coding silent(2)	prostate(1)|stomach(1)	c.G717A						PASS	.	G		1427,2955		150,1127,914	226.0	191.0	203.0		717	-5.3	0.9	15	dbSNP_92	203	4118,4406		767,2584,911	no	coding-synonymous	OR4N4	NM_001005241.2		917,3711,1825	AA,AG,GG		48.3107,32.565,42.9645		239/317	22383189	5545,7361	2191	4262	6453	SO:0001819	synonymous_variant	283694	exon1			GTCCACGTGCACC	AI018459	CCDS32173.1	15q11.2	2012-08-09				ENSG00000183706		"""GPCR / Class A : Olfactory receptors"""	15375	protein-coding gene	gene with protein product							Standard	NM_001005241		Approved		uc010tzv.2	Q8N0Y3		ENST00000328795.4:c.717G>A	15.37:g.22383189G>A		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	85	6	0.0705882	NM_001005241	Q6IEY3|Q6IF56	Silent	SNP	ENST00000328795.4	37	CCDS32173.1																																																																																			G|0.536;A|0.464	0.464	strong		0.493	OR4N4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414922.1		
PCMTD1	115294	hgsc.bcm.edu	37	8	52733227	52733227	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr8:52733227C>T	ENST00000360540.5	-	7	1164	c.758G>A	c.(757-759)cGc>cAc	p.R253H	PCMTD1_ENST00000544451.1_Missense_Mutation_p.R177H|PCMTD1_ENST00000522514.1_Missense_Mutation_p.R253H|PCMTD1_ENST00000519559.1_5'UTR	NM_052937.2	NP_443169.2	Q96MG8	PCMD1_HUMAN	protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 1	253						cytoplasm (GO:0005737)	protein-L-isoaspartate (D-aspartate) O-methyltransferase activity (GO:0004719)	p.R253H(3)		NS(2)|endometrium(1)|kidney(3)|large_intestine(3)|lung(17)|prostate(2)|skin(8)|soft_tissue(1)	37		Lung NSC(129;0.0795)|all_lung(136;0.144)				TCTAAGTGTGCGTCGAATGTA	0.378																																					p.R253H		Atlas-SNP	.											PCMTD1,trunk,malignant_melanoma,0,3	PCMTD1	73	3	3	Substitution - Missense(3)	skin(3)	c.G758A						scavenged	.						66.0	68.0	67.0					8																	52733227		2203	4300	6503	SO:0001583	missense	115294	exon6			AGTGTGCGTCGAA		CCDS6148.1, CCDS69480.1	8q11.23	2010-08-05			ENSG00000168300	ENSG00000168300			30483	protein-coding gene	gene with protein product							Standard	XM_005251146		Approved	FLJ10883	uc003xqx.4	Q96MG8	OTTHUMG00000164246	ENST00000360540.5:c.758G>A	8.37:g.52733227C>T	ENSP00000353739:p.Arg253His	Somatic	234	4	0.017094		WXS	Illumina HiSeq	Phase_I	243	5	0.0205761	NM_052937	Q96FK9	Missense_Mutation	SNP	ENST00000360540.5	37	CCDS6148.1	.	.	.	.	.	.	.	.	.	.	C	17.43	3.387497	0.61956	.	.	ENSG00000168300	ENST00000360540;ENST00000544451;ENST00000522514	T;T;T	0.44083	1.52;0.93;1.52	5.77	5.77	0.91146	.	0.000000	0.85682	D	0.000000	T	0.56031	0.1958	L	0.42245	1.32	0.80722	D	1	P;D;B	0.89917	0.653;1.0;0.051	B;D;B	0.66196	0.059;0.942;0.02	T	0.39623	-0.9605	10	0.20046	T	0.44	-15.7151	19.9832	0.97338	0.0:1.0:0.0:0.0	.	123;177;253	B4E2B4;F5H1M8;Q96MG8	.;.;PCMD1_HUMAN	H	253;177;253	ENSP00000353739:R253H;ENSP00000444026:R177H;ENSP00000428099:R253H	ENSP00000353739:R253H	R	-	2	0	PCMTD1	52895780	1.000000	0.71417	0.998000	0.56505	0.973000	0.67179	7.046000	0.76592	2.722000	0.93159	0.655000	0.94253	CGC	.	.	none		0.378	PCMTD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377909.2	NM_052937	
VN1R2	317701	hgsc.bcm.edu	37	19	53761881	53761881	+	Missense_Mutation	SNP	A	A	C			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr19:53761881A>C	ENST00000341702.3	+	1	337	c.253A>C	c.(253-255)Acc>Ccc	p.T85P		NM_173856.2	NP_776255.2	Q8NFZ6	VN1R2_HUMAN	vomeronasal 1 receptor 2	85					response to pheromone (GO:0019236)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	pheromone receptor activity (GO:0016503)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(6)|lung(15)|skin(1)|upper_aerodigestive_tract(1)	31				GBM - Glioblastoma multiforme(134;0.00301)		agagaaacccaccaaacctgt	0.443																																					p.T85P		Atlas-SNP	.											.	VN1R2	71	.	0			c.A253C						PASS	.						43.0	44.0	44.0					19																	53761881		2193	4285	6478	SO:0001583	missense	317701	exon1			AAACCCACCAAAC	AF370359	CCDS12862.1	19q13.42	2012-08-22			ENSG00000196131	ENSG00000196131		"""Vomeronasal receptors / Type 1"", ""GPCR / Unclassified : Vomeronasal receptors, type 1"""	19872	protein-coding gene	gene with protein product						12123587	Standard	NM_173856		Approved	V1RL2	uc002qbi.2	Q8NFZ6		ENST00000341702.3:c.253A>C	19.37:g.53761881A>C	ENSP00000351244:p.Thr85Pro	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	114	35	0.307018	NM_173856	A1L411|Q8TDU4	Missense_Mutation	SNP	ENST00000341702.3	37	CCDS12862.1	.	.	.	.	.	.	.	.	.	.	A	3.624	-0.076953	0.07184	.	.	ENSG00000196131	ENST00000341702	T	0.10005	2.92	0.0465	0.0465	0.14256	.	.	.	.	.	T	0.04634	0.0126	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.38757	-0.9646	9	0.62326	D	0.03	.	2.1718	0.03851	0.506:2.0E-4:1.0E-4:0.4937	.	85	Q8NFZ6	VN1R2_HUMAN	P	85	ENSP00000351244:T85P	ENSP00000351244:T85P	T	+	1	0	VN1R2	58453693	0.001000	0.12720	0.042000	0.18584	0.043000	0.13939	-0.066000	0.11598	0.115000	0.18071	0.113000	0.15668	ACC	.	.	none		0.443	VN1R2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464285.1	NM_173856	
OR13D1	286365	hgsc.bcm.edu	37	9	107456763	107456763	+	Missense_Mutation	SNP	T	T	C	rs10991359	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr9:107456763T>C	ENST00000318763.5	+	1	104	c.61T>C	c.(61-63)Ttc>Ctc	p.F21L		NM_001004484.1	NP_001004484.1	Q8NGV5	O13D1_HUMAN	olfactory receptor, family 13, subfamily D, member 1	21			F -> L (in dbSNP:rs10991359).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.F21L(1)		large_intestine(4)|lung(10)|ovary(1)|prostate(2)|skin(2)	19						TCATGTCCTTTTCTATACTAC	0.368													T|||	1099	0.219449	0.0106	0.3631	5008	,	,		18835	0.4484		0.2425	False		,,,				2504	0.1401				p.F21L		Atlas-SNP	.											OR13D1,NS,carcinoma,0,1	OR13D1	42	1	1	Substitution - Missense(1)	prostate(1)	c.T61C						scavenged	.	T	LEU/PHE	238,4166	140.0+/-175.5	6,226,1970	65.0	61.0	63.0		61	-5.4	0.0	9	dbSNP_120	63	1834,6766	327.2+/-317.7	209,1416,2675	yes	missense	OR13D1	NM_001004484.1	22	215,1642,4645	CC,CT,TT		21.3256,5.4042,15.9336	benign	21/347	107456763	2072,10932	2202	4300	6502	SO:0001583	missense	286365	exon1			GTCCTTTTCTATA		CCDS35094.1	9q31.1	2013-09-24			ENSG00000179055	ENSG00000179055		"""GPCR / Class A : Olfactory receptors"""	14695	protein-coding gene	gene with protein product							Standard	NM_001004484		Approved		uc011lvs.2	Q8NGV5	OTTHUMG00000020412	ENST00000318763.5:c.61T>C	9.37:g.107456763T>C	ENSP00000317357:p.Phe21Leu	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	105	4	0.0380952	NM_001004484	B9EIS1|Q6IFL1	Missense_Mutation	SNP	ENST00000318763.5	37	CCDS35094.1	582	0.2664835164835165	7	0.014227642276422764	117	0.32320441988950277	261	0.4562937062937063	197	0.2598944591029024	T	10.34	1.323824	0.24080	0.054042	0.213256	ENSG00000179055	ENST00000318763	T	0.00003	9.83	4.08	-5.42	0.02640	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.04165	-1.0972	8	0.27785	T	0.31	.	1.5599	0.02593	0.5009:0.1979:0.1347:0.1665	rs10991359;rs52837362;rs10991359	21	Q8NGV5	O13D1_HUMAN	L	21	ENSP00000317357:F21L	ENSP00000317357:F21L	F	+	1	0	OR13D1	106496584	0.000000	0.05858	0.000000	0.03702	0.520000	0.34377	-1.980000	0.01492	-0.946000	0.03677	0.533000	0.62120	TTC	T|0.800;C|0.200	0.200	strong		0.368	OR13D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053483.1		
SVEP1	79987	hgsc.bcm.edu	37	9	113169631	113169631	+	Missense_Mutation	SNP	G	G	A	rs71492888|rs7030192	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr9:113169631G>A	ENST00000401783.2	-	38	8585	c.8249C>T	c.(8248-8250)gCa>gTa	p.A2750V	SVEP1_ENST00000297826.5_Missense_Mutation_p.A676V|SVEP1_ENST00000374469.1_Missense_Mutation_p.A2727V	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	2750	Sushi 22. {ECO:0000255|PROSITE- ProRule:PRU00302}.		A -> V (in dbSNP:rs7030192). {ECO:0000269|PubMed:14702039}.		cell adhesion (GO:0007155)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|chromatin binding (GO:0003682)			NS(1)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|cervix(2)|endometrium(19)|kidney(8)|large_intestine(24)|lung(58)|ovary(7)|prostate(7)|skin(1)|stomach(4)|upper_aerodigestive_tract(5)|urinary_tract(4)	147						GTCAGAGCCTGCTAGAATGTG	0.458													A|||	2138	0.426917	0.5726	0.3256	5008	,	,		22620	0.4365		0.328	False		,,,				2504	0.3937				p.A2750V		Atlas-SNP	.											.	SVEP1	326	.	0			c.C8249T						PASS	.	A	VAL/ALA	1929,2047		465,999,524	75.0	79.0	78.0		8249	4.7	0.1	9	dbSNP_116	78	2601,5709		391,1819,1945	yes	missense	SVEP1	NM_153366.3	64	856,2818,2469	AA,AG,GG		31.2996,48.5161,36.8712	benign	2750/3572	113169631	4530,7756	1988	4155	6143	SO:0001583	missense	79987	exon38			GAGCCTGCTAGAA	AK027870		9q31-q32	2008-02-05	2005-03-15	2005-03-17	ENSG00000165124	ENSG00000165124			15985	protein-coding gene	gene with protein product		611691	"""chromosome 9 open reading frame 13"""	C9orf13			Standard	NM_153366		Approved	bA427L11.3, POLYDOM, FLJ13529	uc010mtz.3	Q4LDE5	OTTHUMG00000020482	ENST00000401783.2:c.8249C>T	9.37:g.113169631G>A	ENSP00000384917:p.Ala2750Val	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	115	5	0.0434783	NM_153366	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Missense_Mutation	SNP	ENST00000401783.2	37	CCDS48004.1	742	0.33974358974358976	212	0.43089430894308944	108	0.2983425414364641	213	0.3723776223776224	209	0.2757255936675462	A	0	-2.739132	0.00088	0.485161	0.312996	ENSG00000165124	ENST00000401783;ENST00000374469;ENST00000297826;ENST00000374463	T;T;T	0.62364	0.03;0.03;0.03	5.87	4.71	0.59529	Complement control module (2);Sushi/SCR/CCP (3);	0.717443	0.14280	N	0.329611	T	0.00012	0.0000	N	0.00205	-1.85	0.58432	P	1.999999999946489E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.45934	-0.9227	9	0.25106	T	0.35	.	6.1143	0.20117	0.568:0.0:0.0664:0.3656	rs7030192;rs60576083;rs7030192	2750	Q4LDE5	SVEP1_HUMAN	V	2750;2727;676;422	ENSP00000384917:A2750V;ENSP00000363593:A2727V;ENSP00000297826:A676V	ENSP00000297826:A676V	A	-	2	0	SVEP1	112209452	0.005000	0.15991	0.139000	0.22197	0.028000	0.11728	1.821000	0.39041	0.451000	0.26802	-0.352000	0.07741	GCA	A|0.380;G|0.620	0.380	strong		0.458	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
SLC39A4	55630	hgsc.bcm.edu	37	8	145642002	145642002	+	Missense_Mutation	SNP	C	C	T	rs2280838	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr8:145642002C>T	ENST00000301305.3	-	1	277	c.172G>A	c.(172-174)Gcc>Acc	p.A58T	SLC39A4_ENST00000276833.5_5'Flank	NM_130849.2	NP_570901	Q6P5W5	S39A4_HUMAN	solute carrier family 39 (zinc transporter), member 4	58			A -> T (in dbSNP:rs2280838). {ECO:0000269|PubMed:12032886, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		cellular response to zinc ion starvation (GO:0034224)|cellular zinc ion homeostasis (GO:0006882)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|cytoplasmic membrane-bounded vesicle (GO:0016023)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	zinc ion transmembrane transporter activity (GO:0005385)			endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	14	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;1.08e-41)|Epithelial(56;1.12e-40)|all cancers(56;8.17e-36)|BRCA - Breast invasive adenocarcinoma(115;0.0407)|Colorectal(110;0.055)			GGCCCGTTGGCGCAGTGCACA	0.692													C|||	2171	0.433506	0.416	0.4236	5008	,	,		14513	0.373		0.5567	False		,,,				2504	0.3998				p.A58T		Atlas-SNP	.											.	SLC39A4	54	.	0			c.G172A						PASS	.	C	THR/ALA	1886,2490		408,1070,710	22.0	21.0	21.0		172	-9.4	0.0	8	dbSNP_100	21	4892,3694		1419,2054,820	yes	missense	SLC39A4	NM_130849.2	58	1827,3124,1530	TT,TC,CC		43.0235,43.0987,47.7087	benign	58/648	145642002	6778,6184	2188	4293	6481	SO:0001583	missense	55630	exon1			CGTTGGCGCAGTG	AK025537	CCDS6424.1, CCDS43782.1	8q24.3	2013-05-22			ENSG00000147804	ENSG00000147804		"""Solute carriers"""	17129	protein-coding gene	gene with protein product		607059	"""acrodermatitis enteropathica, zinc-deficiency type"""	AEZ		12801924, 12659941, 14709598	Standard	NM_017767		Approved	ZIP4, AWMS2	uc003zcq.3	Q6P5W5		ENST00000301305.3:c.172G>A	8.37:g.145642002C>T	ENSP00000301305:p.Ala58Thr	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	88	6	0.0681818	NM_130849	Q7L5S5|Q9H6T8|Q9NXC4	Missense_Mutation	SNP	ENST00000301305.3	37	CCDS6424.1	1051	0.48122710622710624	205	0.4166666666666667	172	0.47513812154696133	232	0.40559440559440557	442	0.58311345646438	C	15.35	2.807508	0.50421	0.430987	0.569765	ENSG00000147804	ENST00000301305;ENST00000526658	T;T	0.58652	0.32;0.38	4.71	-9.42	0.00610	.	1.979900	0.02592	N	0.100064	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.20907	-1.0261	9	0.10111	T	0.7	-8.2952	5.7065	0.17911	0.1114:0.5786:0.1239:0.1861	rs2280838;rs11553157;rs17855766;rs2280838	58	Q6P5W5	S39A4_HUMAN	T	58	ENSP00000301305:A58T;ENSP00000434512:A58T	ENSP00000301305:A58T	A	-	1	0	SLC39A4	145612810	0.000000	0.05858	0.038000	0.18304	0.845000	0.48019	-2.408000	0.01042	-1.950000	0.01030	-0.683000	0.03753	GCC	C|0.520;T|0.480	0.480	strong		0.692	SLC39A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382688.1		
STRC	161497	hgsc.bcm.edu	37	15	43892847	43892847	+	Silent	SNP	G	G	C	rs12438025	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr15:43892847G>C	ENST00000450892.2	-	26	4955	c.4878C>G	c.(4876-4878)ctC>ctG	p.L1626L	RNU6-554P_ENST00000410466.1_RNA|STRC_ENST00000541030.1_Silent_p.L853L	NM_153700.2	NP_714544.1	Q7RTU9	STRC_HUMAN	stereocilin	1626					auditory receptor cell stereocilium organization (GO:0060088)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)	kinocilium (GO:0060091)|stereocilium bundle tip (GO:0032426)				skin(4)	4		all_cancers(109;3.26e-15)|all_epithelial(112;1.48e-12)|Lung NSC(122;2.76e-08)|all_lung(180;3.1e-07)|Melanoma(134;0.027)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;3.56e-07)		CAGAGCACTGGAGATGCAGGG	0.532													G|||	1475	0.294529	0.556	0.2032	5008	,	,		20056	0.2718		0.0994	False		,,,				2504	0.2301				p.L1626L		Atlas-SNP	.											STRC_ENST00000450892,colon,carcinoma,0,1	STRC	58	1	0			c.C4878G						scavenged	.	G		2041,2359	541.9+/-375.9	485,1071,644	55.0	64.0	61.0		4878	2.9	1.0	15	dbSNP_120	61	846,7748	189.1+/-236.0	50,746,3501	no	coding-synonymous	STRC	NM_153700.2		535,1817,4145	CC,CG,GG		9.8441,46.3864,22.2179		1626/1776	43892847	2887,10107	2200	4297	6497	SO:0001819	synonymous_variant	161497	exon26			GCACTGGAGATGC	BK000138	CCDS10098.1	15q15.3	2010-02-26			ENSG00000242866	ENSG00000242866			16035	protein-coding gene	gene with protein product		606440		DFNB16		11687802, 9429146	Standard	NM_153700		Approved		uc001zsf.3	Q7RTU9	OTTHUMG00000059899	ENST00000450892.2:c.4878C>G	15.37:g.43892847G>C		Somatic	217	0	0		WXS	Illumina HiSeq	Phase_I	199	4	0.0201005	NM_153700		Silent	SNP	ENST00000450892.2	37	CCDS10098.1																																																																																			G|0.784;C|0.216	0.216	strong		0.532	STRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133140.1	NM_153700	
TLR1	7096	hgsc.bcm.edu	37	4	38798935	38798935	+	Silent	SNP	C	C	T	rs5743614	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr4:38798935C>T	ENST00000502213.2	-	3	1747	c.1518G>A	c.(1516-1518)tcG>tcA	p.S506S	TLR1_ENST00000510552.1_5'Flank|TLR1_ENST00000308979.2_Silent_p.S506S			Q15399	TLR1_HUMAN	toll-like receptor 1	506					cellular response to triacyl bacterial lipopeptide (GO:0071727)|detection of triacyl bacterial lipopeptide (GO:0042495)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|macrophage activation (GO:0042116)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of interleukin-6 biosynthetic process (GO:0045410)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|regulation of cytokine secretion (GO:0050707)|signal transduction (GO:0007165)|toll-like receptor 1 signaling pathway (GO:0034130)	cytoplasmic vesicle (GO:0031410)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|Toll-like receptor 1-Toll-like receptor 2 protein complex (GO:0035354)	protein heterodimerization activity (GO:0046982)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|skin(4)|stomach(2)	28						AGAAATCAGCCGATGGGTGGG	0.418													c|||	2802	0.559505	0.8404	0.4654	5008	,	,		18263	0.5992		0.2744	False		,,,				2504	0.499				p.S506S	GBM(5;216 373 40795 46382)	Atlas-SNP	.											TLR1,NS,carcinoma,-1,1	TLR1	70	1	0			c.G1518A						scavenged	.						75.0	79.0	78.0					4																	38798935		2202	4280	6482	SO:0001819	synonymous_variant	7096	exon4			ATCAGCCGATGGG	U88540	CCDS33973.1	4p14	2008-02-05				ENSG00000174125		"""CD molecules"""	11847	protein-coding gene	gene with protein product		601194				9435236, 7584026	Standard	NM_003263		Approved	rsc786, KIAA0012, CD281	uc003gtl.3	Q15399		ENST00000502213.2:c.1518G>A	4.37:g.38798935C>T		Somatic	163	1	0.00613497		WXS	Illumina HiSeq	Phase_I	198	8	0.040404	NM_003263	D1CS39|D1CS41|O15452|Q32MK3|Q32MK4|Q9UG90	Silent	SNP	ENST00000502213.2	37	CCDS33973.1																																																																																			C|0.575;T|0.425	0.425	strong		0.418	TLR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360510.3		
UGT2B7	7364	hgsc.bcm.edu	37	4	69962449	69962449	+	Missense_Mutation	SNP	G	G	T	rs12233719	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr4:69962449G>T	ENST00000508661.1	+	1	238	c.211G>T	c.(211-213)Gct>Tct	p.A71S	UGT2B7_ENST00000509763.1_Intron|UGT2B7_ENST00000305231.7_Missense_Mutation_p.A71S			P16662	UD2B7_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide B7	71			A -> S (in dbSNP:rs12233719).		androgen metabolic process (GO:0008209)|cellular glucuronidation (GO:0052695)|lipid metabolic process (GO:0006629)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	glucuronosyltransferase activity (GO:0015020)			autonomic_ganglia(1)|endometrium(3)|kidney(4)|large_intestine(6)|lung(16)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	38					Atorvastatin(DB01076)|Carbamazepine(DB00564)|Chenodeoxycholic acid(DB06777)|Codeine(DB00318)|Dabigatran etexilate(DB06695)|Dapagliflozin(DB06292)|Diclofenac(DB00586)|Epirubicin(DB00445)|Etodolac(DB00749)|Ezetimibe(DB00973)|Flunitrazepam(DB01544)|Flurbiprofen(DB00712)|Fluvastatin(DB01095)|Ibuprofen(DB01050)|Indomethacin(DB00328)|Losartan(DB00678)|Lovastatin(DB00227)|Mitiglinide(DB01252)|Morphine(DB00295)|Mycophenolate mofetil(DB00688)|Mycophenolic acid(DB01024)|Naproxen(DB00788)|Oxazepam(DB00842)|Pitavastatin(DB08860)|Silodosin(DB06207)|Simvastatin(DB00641)|Suprofen(DB00870)|Tapentadol(DB06204)|Valproic Acid(DB00313)|Zidovudine(DB00495)	CAACTCATCCGCTCTTAAAAT	0.378													G|||	149	0.0297524	0.0008	0.0058	5008	,	,		18847	0.1319		0.004	False		,,,				2504	0.0072				p.A71S		Atlas-SNP	.											.	UGT2B7	79	.	0			c.G211T	GRCh37	CM077880	UGT2B7	M	rs12233719	PASS	.	G	SER/ALA	1,4405	2.1+/-5.4	0,1,2202	70.0	76.0	74.0		211	-3.9	0.0	4	dbSNP_120	74	3,8593	3.7+/-12.6	0,3,4295	yes	missense	UGT2B7	NM_001074.2	99	0,4,6497	TT,TG,GG		0.0349,0.0227,0.0308	benign	71/530	69962449	4,12998	2203	4298	6501	SO:0001583	missense	7364	exon1			TCATCCGCTCTTA	BC030974	CCDS3526.1	4q13	2008-02-05	2005-07-20		ENSG00000171234	ENSG00000171234		"""UDP glucuronosyltransferases"""	12554	protein-coding gene	gene with protein product		600068	"""UDP glycosyltransferase 2 family, polypeptide B7"""			2159463, 7835904	Standard	NM_001074		Approved	UGT2B9	uc003heg.4	P16662	OTTHUMG00000129404	ENST00000508661.1:c.211G>T	4.37:g.69962449G>T	ENSP00000427659:p.Ala71Ser	Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	169	7	0.0414201	NM_001074	B2R810|Q6GTW0	Missense_Mutation	SNP	ENST00000508661.1	37		86	0.039377289377289376	1	0.0020325203252032522	4	0.011049723756906077	76	0.13286713286713286	5	0.006596306068601583	G	1.462	-0.562049	0.03939	2.27E-4	3.49E-4	ENSG00000171234	ENST00000305231;ENST00000508661	T;T	0.62232	0.04;0.04	2.54	-3.88	0.04205	.	0.292897	0.27012	U	0.021361	T	0.00440	0.0014	N	0.12887	0.27	0.09310	N	1	B;B	0.25809	0.135;0.119	B;B	0.42653	0.394;0.142	T	0.25847	-1.0120	9	.	.	.	.	1.1215	0.01725	0.3155:0.1491:0.3838:0.1516	rs12233719;rs52806684;rs58730779;rs12233719	71;71	E9PBP8;P16662	.;UD2B7_HUMAN	S	71	ENSP00000304811:A71S;ENSP00000427659:A71S	.	A	+	1	0	UGT2B7	69997038	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-1.559000	0.02162	-1.439000	0.01962	-1.806000	0.00616	GCT	A|0.000;G|0.986;T|0.013	0.013	strong		0.378	UGT2B7-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000362103.1	NM_001074	
CYP2D6	1565	hgsc.bcm.edu	37	22	42522613	42522613	+	Missense_Mutation	SNP	G	G	C	rs1135840	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr22:42522613G>C	ENST00000360608.5	-	9	1571	c.1457C>G	c.(1456-1458)aCc>aGc	p.T486S	NDUFA6-AS1_ENST00000416037.2_RNA|NDUFA6-AS1_ENST00000439129.1_RNA|NDUFA6-AS1_ENST00000610250.1_RNA|CYP2D6_ENST00000389970.3_Missense_Mutation_p.T486S|NDUFA6-AS1_ENST00000536447.2_RNA|CYP2D6_ENST00000359033.4_Missense_Mutation_p.T435S|NDUFA6-AS1_ENST00000600968.1_RNA|NDUFA6-AS1_ENST00000451451.1_RNA|NDUFA6-AS1_ENST00000595777.1_RNA|NDUFA6-AS1_ENST00000434834.1_RNA|NDUFA6-AS1_ENST00000417327.1_RNA	NM_000106.5	NP_000097	P10635	CP2D6_HUMAN	cytochrome P450, family 2, subfamily D, polypeptide 6	486			S -> T (in allele CYP2D6*2, allele CYP2D6*10, allele CYP2D6*12, allele CYP2D6*14, allele CYP2D6*17, allele CYP2D6*45A, allele CYP2D6*45B and allele CYP2D6*46; impaired metabolism of sparteine; dbSNP:rs1135840). {ECO:0000269|PubMed:10591208, ECO:0000269|PubMed:15469410, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:15768052, ECO:0000269|PubMed:8287064}.		alkaloid catabolic process (GO:0009822)|alkaloid metabolic process (GO:0009820)|coumarin metabolic process (GO:0009804)|drug catabolic process (GO:0042737)|drug metabolic process (GO:0017144)|heterocycle metabolic process (GO:0046483)|isoquinoline alkaloid metabolic process (GO:0033076)|monoterpenoid metabolic process (GO:0016098)|negative regulation of binding (GO:0051100)|negative regulation of cellular organofluorine metabolic process (GO:0090350)|oxidation-reduction process (GO:0055114)|oxidative demethylation (GO:0070989)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|mitochondrion (GO:0005739)	aromatase activity (GO:0070330)|drug binding (GO:0008144)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity (GO:0016491)			NS(1)|breast(2)|endometrium(1)|large_intestine(2)|lung(4)|prostate(7)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	21					Abiraterone(DB05812)|Acebutolol(DB01193)|Acetaminophen(DB00316)|Ajmaline(DB01426)|Almotriptan(DB00918)|Alogliptin(DB06203)|Alprenolol(DB00866)|Aminophenazone(DB01424)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Amodiaquine(DB00613)|Amoxapine(DB00543)|Amphetamine(DB00182)|Amprenavir(DB00701)|Amsacrine(DB00276)|Antipyrine(DB01435)|Aprindine(DB01429)|Arformoterol(DB01274)|Aripiprazole(DB01238)|Artemether(DB06697)|Asenapine(DB06216)|Astemizole(DB00637)|Atomoxetine(DB00289)|Atorvastatin(DB01076)|Azelastine(DB00972)|Benzatropine(DB00245)|Benzyl alcohol(DB06770)|Bepridil(DB01244)|Betaxolol(DB00195)|Bicalutamide(DB01128)|Biperiden(DB00810)|Bisoprolol(DB00612)|Bortezomib(DB00188)|Brompheniramine(DB00835)|Bupivacaine(DB00297)|Buprenorphine(DB00921)|Bupropion(DB01156)|Buspirone(DB00490)|Caffeine(DB00201)|Captopril(DB01197)|Carbinoxamine(DB00748)|Carteolol(DB00521)|Carvedilol(DB01136)|Celecoxib(DB00482)|Cephalexin(DB00567)|Cevimeline(DB00185)|Chlordiazepoxide(DB00475)|Chloroquine(DB00608)|Chlorphenamine(DB01114)|Chlorpromazine(DB00477)|Chlorzoxazone(DB00356)|Cholecalciferol(DB00169)|Ciclesonide(DB01410)|Cilostazol(DB01166)|Cimetidine(DB00501)|Cinacalcet(DB01012)|Cinnarizine(DB00568)|Cisapride(DB00604)|Citalopram(DB00215)|Clemastine(DB00283)|Clevidipine(DB04920)|Clomipramine(DB01242)|Clonidine(DB00575)|Clotrimazole(DB00257)|Clozapine(DB00363)|Cocaine(DB00907)|Codeine(DB00318)|Cyclobenzaprine(DB00924)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dapagliflozin(DB06292)|Darifenacin(DB00496)|Debrisoquin(DB04840)|Delavirdine(DB00705)|Desipramine(DB01151)|Desloratadine(DB00967)|Dexamethasone(DB01234)|Dexfenfluramine(DB01191)|Dexmedetomidine(DB00633)|Dexmethylphenidate(DB06701)|Dextroamphetamine(DB01576)|Dextromethorphan(DB00514)|Dextropropoxyphene(DB00647)|Dihydrocodeine(DB01551)|Diltiazem(DB00343)|Dimethyl sulfoxide(DB01093)|Diphenhydramine(DB01075)|Dolasetron(DB00757)|Domperidone(DB01184)|Donepezil(DB00843)|Dopamine(DB00988)|Doxazosin(DB00590)|Doxepin(DB01142)|Doxorubicin(DB00997)|Dronedarone(DB04855)|Duloxetine(DB00476)|Efavirenz(DB00625)|Eletriptan(DB00216)|Encainide(DB01228)|Enzalutamide(DB08899)|Epinastine(DB00751)|Erlotinib(DB00530)|Escitalopram(DB01175)|Ethylmorphine(DB01466)|Etoricoxib(DB01628)|Felodipine(DB01023)|Fesoterodine(DB06702)|Fexofenadine(DB00950)|Fingolimod(DB08868)|Flecainide(DB01195)|Flunarizine(DB04841)|Fluoxetine(DB00472)|Fluphenazine(DB00623)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Formoterol(DB00983)|Galantamine(DB00674)|Gefitinib(DB00317)|Glutethimide(DB01437)|Granisetron(DB00889)|Halofantrine(DB01218)|Haloperidol(DB00502)|Halothane(DB01159)|Histamine Phosphate(DB00667)|Hydrocodone(DB00956)|Hydromorphone(DB00327)|Hydroxychloroquine(DB01611)|Hydroxyurea(DB01005)|Hydroxyzine(DB00557)|Idarubicin(DB01177)|Iloperidone(DB04946)|Imatinib(DB00619)|Imipramine(DB00458)|Indinavir(DB00224)|Ipratropium bromide(DB00332)|Irbesartan(DB01029)|Isoniazid(DB00951)|Itraconazole(DB01167)|Ketoconazole(DB01026)|L-DOPA(DB01235)|Labetalol(DB00598)|Lansoprazole(DB00448)|Lercanidipine(DB00528)|Levomilnacipran(DB08918)|Lidocaine(DB00281)|Lisuride(DB00589)|Lomustine(DB01206)|Loperamide(DB00836)|Lopinavir(DB01601)|Loratadine(DB00455)|Lorcaserin(DB04871)|Lovastatin(DB00227)|Lumefantrine(DB06708)|Maprotiline(DB00934)|Mefloquine(DB00358)|Mepyramine(DB06691)|Mequitazine(DB01071)|Mesoridazine(DB00933)|Methadone(DB00333)|Methamphetamine(DB01577)|Methazolamide(DB00703)|Methimazole(DB00763)|Methotrimeprazine(DB01403)|Methoxyflurane(DB01028)|Methylnaltrexone(DB06800)|Methylphenidate(DB00422)|Methyprylon(DB01107)|Metoclopramide(DB01233)|Metoprolol(DB00264)|Mexiletine(DB00379)|Mianserin(DB06148)|Miconazole(DB01110)|Midodrine(DB00211)|Mifepristone(DB00834)|Minaprine(DB00805)|Mirabegron(DB08893)|Mirtazapine(DB00370)|Moclobemide(DB01171)|Morphine(DB00295)|Nateglinide(DB00731)|Nebivolol(DB04861)|Nefazodone(DB01149)|Nelfinavir(DB00220)|Nevirapine(DB00238)|Niacin(DB00627)|Nicardipine(DB00622)|Nicergoline(DB00699)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilotinib(DB04868)|Nitrofural(DB00336)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Omeprazole(DB00338)|Ondansetron(DB00904)|Oxamniquine(DB01096)|Oxprenolol(DB01580)|Oxybutynin(DB01062)|Oxycodone(DB00497)|Oxymorphone(DB01192)|Paliperidone(DB01267)|Palonosetron(DB00377)|Paroxetine(DB00715)|Pazopanib(DB06589)|Pentamidine(DB00738)|Pergolide(DB01186)|Perhexiline(DB01074)|Perphenazine(DB00850)|Pethidine(DB00454)|Phenformin(DB00914)|Phentermine(DB00191)|Pimozide(DB01100)|Pindolol(DB00960)|Pioglitazone(DB01132)|Piperazine(DB00592)|Pipotiazine(DB01621)|Ponatinib(DB08901)|Pravastatin(DB00175)|Praziquantel(DB01058)|Primaquine(DB01087)|Procainamide(DB01035)|Prochlorperazine(DB00433)|Progesterone(DB00396)|Proguanil(DB01131)|Promethazine(DB01069)|Propafenone(DB01182)|Propofol(DB00818)|Propranolol(DB00571)|Protriptyline(DB00344)|Pseudoephedrine(DB00852)|Pyrimethamine(DB00205)|Quetiapine(DB01224)|Quinidine(DB00908)|Quinine(DB00468)|Rabeprazole(DB01129)|Ranitidine(DB00863)|Ranolazine(DB00243)|Reboxetine(DB00234)|Remoxipride(DB00409)|Rifapentine(DB01201)|Risperidone(DB00734)|Ritonavir(DB00503)|Rivastigmine(DB00989)|Ropinirole(DB00268)|Ropivacaine(DB00296)|Rosiglitazone(DB00412)|Rotigotine(DB05271)|Saquinavir(DB01232)|Selegiline(DB01037)|Sertindole(DB06144)|Sertraline(DB01104)|Sildenafil(DB00203)|Simvastatin(DB00641)|Sorafenib(DB00398)|Sulfanilamide(DB00259)|Sulfaphenazole(DB06729)|Tamoxifen(DB00675)|Tamsulosin(DB00706)|Tapentadol(DB06204)|Telithromycin(DB00976)|Temsirolimus(DB06287)|Terbinafine(DB00857)|Tetrabenazine(DB04844)|Theophylline(DB00277)|Thioridazine(DB00679)|Thiothixene(DB01623)|Ticlopidine(DB00208)|Timolol(DB00373)|Tiotropium(DB01409)|Tipranavir(DB00932)|Tolterodine(DB01036)|Trabectedin(DB05109)|Tramadol(DB00193)|Tranylcypromine(DB00752)|Trazodone(DB00656)|Trimipramine(DB00726)|Tripelennamine(DB00792)|Triprolidine(DB00427)|Trospium(DB00209)|Vemurafenib(DB08881)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vilazodone(DB06684)|Vinblastine(DB00570)|Vinorelbine(DB00361)|Yohimbine(DB01392)|Zafirlukast(DB00549)|Zalcitabine(DB00943)|Ziprasidone(DB00246)|Zolpidem(DB00425)	GGGGGATGGGGTCACCAGGAA	0.577													G|||	2009	0.401158	0.3238	0.5245	5008	,	,		18454	0.2956		0.4543	False		,,,				2504	0.4724				p.T486S		Atlas-SNP	.											CYP2D6_ENST00000360608,brain,glioma,0,2	CYP2D6	104	2	0			c.C1457G	GRCh37	CM931123	CYP2D6	M	rs1135840	scavenged	.	G	SER/THR,SER/THR	1594,2790	468.1+/-355.0	356,882,954	34.0	31.0	32.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1457,1304	-2.7	0.0	22	dbSNP_86	32	3706,4890	501.7+/-375.5	881,1944,1473	yes	missense,missense	CYP2D6	NM_000106.4,NM_001025161.1	58,58	1237,2826,2427	CC,CG,GG		43.1131,36.3595,40.832	benign,benign	486/498,435/447	42522613	5300,7680	2192	4298	6490	SO:0001583	missense	1565	exon9			GATGGGGTCACCA	M20403	CCDS33657.1, CCDS46721.1	22q13.1	2014-09-17	2003-01-14		ENSG00000100197	ENSG00000100197		"""Cytochrome P450s"""	2625	protein-coding gene	gene with protein product		124030	"""cytochrome P450, subfamily IID (debrisoquine, sparteine, etc., -metabolizing), polypeptide 6"", ""cytochrome P450, family 2, subfamily D, polypeptide 7 pseudogene 2"", ""cytochrome P450, subfamily II (debrisoquine, sparteine, etc., -metabolising), polypeptide 7 pseudogene 2"", ""cytochrome P450, family 2, subfamily D, polypeptide 8 pseudogene 2"", ""cytochrome P450, subfamily IID (debrisoquine, sparteine, etc., -metabolising), polypeptide 8 pseudogene 2"""	CYP2DL1, CYP2D7P2, CYP2D7BP, CYP2D8P2, CYP2D7AP		8449513	Standard	NM_000106		Approved	CPD6, P450-DB1, CYP2D, P450C2D	uc003bce.3	P10635	OTTHUMG00000150918	ENST00000360608.5:c.1457C>G	22.37:g.42522613G>C	ENSP00000353820:p.Thr486Ser	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	126	3	0.0238095	NM_000106	Q16752|Q2XND6|Q2XND7|Q2XNE0|Q6B012|Q6NXU8	Missense_Mutation	SNP	ENST00000360608.5	37	CCDS46721.1	877	0.4015567765567766	156	0.3170731707317073	188	0.5193370165745856	190	0.3321678321678322	343	0.4525065963060686	G	3.127	-0.179188	0.06380	0.363595	0.431131	ENSG00000100197	ENST00000360608;ENST00000389970;ENST00000413640;ENST00000359033;ENST00000542856	T;T;T	0.68765	-0.35;-0.35;5.1	4.85	-2.65	0.06095	.	1.222600	0.05550	N	0.567358	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B;B;B	0.17038	0.02;0.02;0.02	B;B;B	0.18871	0.023;0.023;0.023	T	0.32798	-0.9893	8	0.08381	T	0.77	.	5.2556	0.15546	0.4162:0.2592:0.3246:0.0	rs1135840;rs57862116	486;435;486	C1ID54;Q6NXU8;Q6NWU0	.;.;.	S	486;486;432;435;435	ENSP00000353820:T486S;ENSP00000374620:T486S;ENSP00000351927:T435S	ENSP00000351927:T435S	T	-	2	0	CYP2D6	40852557	0.080000	0.21391	0.001000	0.08648	0.004000	0.04260	0.361000	0.20267	-0.465000	0.06953	-0.315000	0.08773	ACC	G|0.600;C|0.400	0.400	strong		0.577	CYP2D6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320525.1		
RNF111	54778	hgsc.bcm.edu	37	15	59347929	59347929	+	Silent	SNP	C	C	A	rs1446239	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr15:59347929C>A	ENST00000557998.1	+	4	1343	c.1056C>A	c.(1054-1056)tcC>tcA	p.S352S	RNF111_ENST00000434298.1_Silent_p.S352S|RNF111_ENST00000561186.1_Silent_p.S352S|RNF111_ENST00000559209.1_Silent_p.S352S|RNF111_ENST00000348370.4_Silent_p.S352S	NM_001270530.1	NP_001257459.1	Q6ZNA4	RN111_HUMAN	ring finger protein 111	352	Interaction with AXIN1.|Ser-rich.				gene expression (GO:0010467)|pattern specification process (GO:0007389)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|protein polyubiquitination (GO:0000209)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ubiquitin-dependent SMAD protein catabolic process (GO:0030579)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	ligase activity (GO:0016874)|SUMO polymer binding (GO:0032184)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|lung(11)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	35				all cancers(107;0.194)		GCCAGGGTTCCAGTTCTCATG	0.433													A|||	2212	0.441693	0.6611	0.4986	5008	,	,		16383	0.4405		0.3161	False		,,,				2504	0.2352				p.S352S	NSCLC(72;983 1365 10746 34387 47081)	Atlas-SNP	.											RNF111_ENST00000434298,rectum,carcinoma,0,4	RNF111	179	4	0			c.C1056A						PASS	.	A		2723,1661	505.6+/-366.2	863,997,332	56.0	48.0	51.0		1056	-0.0	1.0	15	dbSNP_88	51	3016,5566	661.7+/-401.9	560,1896,1835	yes	coding-synonymous	RNF111	NM_017610.6		1423,2893,2167	AA,AC,CC		35.1433,37.8878,44.2619		352/987	59347929	5739,7227	2192	4291	6483	SO:0001819	synonymous_variant	54778	exon4			GGGTTCCAGTTCT	AL157474	CCDS10169.1, CCDS58365.1, CCDS58366.1	15q21	2013-01-09			ENSG00000157450	ENSG00000157450		"""RING-type (C3HC4) zinc fingers"""	17384	protein-coding gene	gene with protein product		605840				11298452	Standard	NM_017610		Approved	ARK, Arkadia, FLJ38008, DKFZP761D081	uc002aft.4	Q6ZNA4	OTTHUMG00000132716	ENST00000557998.1:c.1056C>A	15.37:g.59347929C>A		Somatic	226	0	0		WXS	Illumina HiSeq	Phase_I	211	12	0.056872	NM_017610	C9JUS4|H0YN55|Q6P9A4|Q6ZMU2|Q7L428|Q7Z346|Q8N1P9|Q8WUA3|Q9NSR1	Silent	SNP	ENST00000557998.1	37	CCDS58366.1																																																																																			C|0.554;A|0.446	0.446	strong		0.433	RNF111-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000416012.1	NM_017610	
TDRD9	122402	hgsc.bcm.edu	37	14	104452640	104452640	+	Silent	SNP	G	G	A	rs10143389	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr14:104452640G>A	ENST00000409874.4	+	8	1146	c.1098G>A	c.(1096-1098)ttG>ttA	p.L366L	TDRD9_ENST00000339063.5_Silent_p.L366L	NM_153046.2	NP_694591.2	Q8NDG6	TDRD9_HUMAN	tudor domain containing 9	366					cell differentiation (GO:0030154)|DNA methylation involved in gamete generation (GO:0043046)|fertilization (GO:0009566)|gene silencing by RNA (GO:0031047)|male meiosis (GO:0007140)|multicellular organismal development (GO:0007275)|piRNA metabolic process (GO:0034587)|spermatogenesis (GO:0007283)	nucleus (GO:0005634)|piP-body (GO:0071547)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)	p.L366L(1)|p.L81L(1)		breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(10)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)	33		all_cancers(154;0.109)|Melanoma(154;0.0525)|all_epithelial(191;0.0768)				TTGATGACTTGGATATGAAGG	0.348													G|||	1613	0.322085	0.2731	0.3516	5008	,	,		18906	0.3343		0.3588	False		,,,				2504	0.317				p.L366L		Atlas-SNP	.											TDRD9_ENST00000409874,NS,carcinoma,0,2	TDRD9	175	2	2	Substitution - coding silent(2)	stomach(2)	c.G1098A						scavenged	.	G		1326,3080	446.7+/-348.1	190,946,1067	113.0	104.0	107.0		1098	3.9	1.0	14	dbSNP_119	107	2984,5616	460.9+/-365.3	518,1948,1834	no	coding-synonymous	TDRD9	NM_153046.2		708,2894,2901	AA,AG,GG		34.6977,30.0953,33.1386		366/1383	104452640	4310,8696	2203	4300	6503	SO:0001819	synonymous_variant	122402	exon8			TGACTTGGATATG	AK093483	CCDS9987.2	14q32.33	2013-01-23	2004-04-01	2004-04-02	ENSG00000156414	ENSG00000156414		"""Tudor domain containing"""	20122	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 75"""	C14orf75			Standard	NM_153046		Approved	DKFZp434N0820, FLJ36164, NET54	uc001yom.4	Q8NDG6	OTTHUMG00000152876	ENST00000409874.4:c.1098G>A	14.37:g.104452640G>A		Somatic	168	2	0.0119048		WXS	Illumina HiSeq	Phase_I	185	7	0.0378378	NM_153046	A1A4S7|Q6ZU54|Q8N7T3|Q8N827|Q8N9V5|Q96AS9	Silent	SNP	ENST00000409874.4	37	CCDS9987.2	706	0.3232600732600733	131	0.266260162601626	118	0.3259668508287293	183	0.31993006993006995	274	0.36147757255936674	G	8.454	0.853663	0.17106	0.300953	0.346977	ENSG00000156414	ENST00000557332	.	.	.	5.71	3.9	0.45041	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.38200	-0.9672	3	.	.	.	.	7.929	0.29891	0.25:0.0:0.75:0.0	rs10143389;rs58504835;rs10143389	.	.	.	R	93	.	.	G	+	1	0	TDRD9	103522393	1.000000	0.71417	0.986000	0.45419	0.988000	0.76386	1.987000	0.40687	0.772000	0.33382	0.650000	0.86243	GGA	G|0.674;A|0.326	0.326	strong		0.348	TDRD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328325.3	NM_153046	
OR1A2	26189	hgsc.bcm.edu	37	17	3101691	3101691	+	Missense_Mutation	SNP	G	G	T	rs12150427	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr17:3101691G>T	ENST00000381951.1	+	1	879	c.879G>T	c.(877-879)tgG>tgT	p.W293C		NM_012352.1	NP_036484.1	Q9Y585	OR1A2_HUMAN	olfactory receptor, family 1, subfamily A, member 2	293			W -> C (in dbSNP:rs12150427). {ECO:0000269|PubMed:15489334}.		positive regulation of cytokinesis (GO:0032467)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.W293C(1)		breast(1)|endometrium(4)|large_intestine(2)|lung(5)|skin(4)|stomach(2)	18						TGAGAAATTGGGATATGAAGG	0.463													G|||	1447	0.288938	0.0598	0.2853	5008	,	,		18238	0.5595		0.3509	False		,,,				2504	0.2587				p.W293C		Atlas-SNP	.											OR1A2,NS,carcinoma,0,1	OR1A2	52	1	1	Substitution - Missense(1)	stomach(1)	c.G879T						PASS	.	G	CYS/TRP	506,3900	232.3+/-245.9	33,440,1730	102.0	102.0	102.0		879	-3.0	0.0	17	dbSNP_120	102	3181,5419	476.1+/-369.3	595,1991,1714	yes	missense	OR1A2	NM_012352.1	215	628,2431,3444	TT,TG,GG		36.9884,11.4843,28.3485	benign	293/310	3101691	3687,9319	2203	4300	6503	SO:0001583	missense	26189	exon1			AAATTGGGATATG	AF155225	CCDS11021.1	17p13.3	2012-08-09			ENSG00000172150	ENSG00000172150		"""GPCR / Class A : Olfactory receptors"""	8180	protein-coding gene	gene with protein product						10673334	Standard	NM_012352		Approved	OR17-6	uc002fvd.1	Q9Y585	OTTHUMG00000090638	ENST00000381951.1:c.879G>T	17.37:g.3101691G>T	ENSP00000371377:p.Trp293Cys	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	101	8	0.0792079	NM_012352	Q3KPH3|Q6IFM0|Q6NTD8|Q96R86	Missense_Mutation	SNP	ENST00000381951.1	37	CCDS11021.1	731	0.3347069597069597	35	0.07113821138211382	119	0.3287292817679558	313	0.5472027972027972	264	0.3482849604221636	G	0.906	-0.720596	0.03182	0.114843	0.369884	ENSG00000172150	ENST00000381951	T	0.37058	1.22	4.0	-3.05	0.05396	.	0.337248	0.21566	N	0.072494	T	0.00012	0.0000	N	0.14661	0.345	0.41321	P	0.012827000000000033	B	0.13145	0.007	B	0.06405	0.002	T	0.45775	-0.9238	9	0.87932	D	0	.	5.0262	0.14385	0.5003:0.0:0.3583:0.1413	rs12150427;rs17822470;rs52823271;rs60260068;rs12150427	293	Q9Y585	OR1A2_HUMAN	C	293	ENSP00000371377:W293C	ENSP00000371377:W293C	W	+	3	0	OR1A2	3048441	0.000000	0.05858	0.020000	0.16555	0.009000	0.06853	-0.330000	0.07925	-0.665000	0.05317	0.543000	0.68304	TGG	G|0.697;N|0.000	.	strong		0.463	OR1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207293.1	NM_012352	
CACNA2D3	55799	hgsc.bcm.edu	37	3	54880461	54880461	+	Silent	SNP	A	A	G	rs3773603	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr3:54880461A>G	ENST00000474759.1	+	17	1641	c.1593A>G	c.(1591-1593)ggA>ggG	p.G531G	CACNA2D3_ENST00000415676.2_Silent_p.G531G|CACNA2D3_ENST00000490478.1_Silent_p.G437G|CACNA2D3_ENST00000288197.5_Silent_p.G531G	NM_018398.2	NP_060868.2	Q8IZS8	CA2D3_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 3	531	Cache.					integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(17)|ovary(1)|prostate(1)|skin(5)|stomach(1)|urinary_tract(3)	59				KIRC - Kidney renal clear cell carcinoma(284;0.00287)|Kidney(284;0.00327)	Amlodipine(DB00381)|Nilvadipine(DB06712)|Spironolactone(DB00421)	CAAATAATGGATATATCCTGA	0.383													A|||	837	0.167133	0.112	0.1873	5008	,	,		17618	0.1786		0.1938	False		,,,				2504	0.1881				p.G531G		Atlas-SNP	.											.	CACNA2D3	159	.	0			c.A1593G						PASS	.	A		497,3269		34,429,1420	86.0	82.0	83.0		1593	1.2	1.0	3	dbSNP_107	83	1533,6683		142,1249,2717	no	coding-synonymous	CACNA2D3	NM_018398.2		176,1678,4137	GG,GA,AA		18.6587,13.197,16.9421		531/1092	54880461	2030,9952	1883	4108	5991	SO:0001819	synonymous_variant	55799	exon17			TAATGGATATATC	AJ272268	CCDS54598.1	3p21.1	2010-10-05	2008-02-26		ENSG00000157445	ENSG00000157445		"""Calcium channel subunits"""	15460	protein-coding gene	gene with protein product		606399				11245980	Standard	XM_005265318		Approved	HSA272268	uc003dhf.3	Q8IZS8	OTTHUMG00000158580	ENST00000474759.1:c.1593A>G	3.37:g.54880461A>G		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	122	5	0.0409836	NM_018398	B2RPL6|Q9NY16|Q9NY18	Silent	SNP	ENST00000474759.1	37	CCDS54598.1																																																																																			A|0.825;G|0.175	0.175	strong		0.383	CACNA2D3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351402.1		
MMP27	64066	hgsc.bcm.edu	37	11	102563739	102563739	+	Silent	SNP	C	C	T	rs1276289	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr11:102563739C>T	ENST00000260229.4	-	9	1318	c.1227G>A	c.(1225-1227)ggG>ggA	p.G409G		NM_022122.2	NP_071405.2	Q9H306	MMP27_HUMAN	matrix metallopeptidase 27	409					collagen catabolic process (GO:0030574)	proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(2)|lung(12)|ovary(2)|prostate(2)|skin(11)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	45	all_cancers(8;0.000843)|all_epithelial(12;0.00362)|Lung NSC(15;0.21)	all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)	Epithelial(9;0.0509)|Lung(13;0.0696)|LUSC - Lung squamous cell carcinoma(19;0.13)|all cancers(10;0.176)	BRCA - Breast invasive adenocarcinoma(274;0.0151)	Marimastat(DB00786)	TCTGCGGGAACCCTTTGTCCA	0.438													C|||	2254	0.45008	0.2186	0.5072	5008	,	,		19176	0.629		0.4453	False		,,,				2504	0.5429				p.G409G		Atlas-SNP	.											MMP27,NS,carcinoma,0,1	MMP27	84	1	0			c.G1227A						PASS	.	C		1205,3201	419.8+/-338.8	150,905,1148	193.0	181.0	185.0		1227	-5.4	0.3	11	dbSNP_87	185	3891,4707	544.7+/-384.6	858,2175,1266	no	coding-synonymous	MMP27	NM_022122.2		1008,3080,2414	TT,TC,CC		45.2547,27.3491,39.1879		409/514	102563739	5096,7908	2203	4299	6502	SO:0001819	synonymous_variant	64066	exon9			CGGGAACCCTTTG	AF195192	CCDS8319.1	11q24	2008-07-18	2005-08-08		ENSG00000137675	ENSG00000137675			14250	protein-coding gene	gene with protein product	"""matrix metalloprotease 27"""		"""matrix metalloproteinase 27"""			10419448	Standard	NM_022122		Approved		uc001phd.1	Q9H306	OTTHUMG00000168099	ENST00000260229.4:c.1227G>A	11.37:g.102563739C>T		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	125	6	0.048	NM_022122	Q6UWK6	Silent	SNP	ENST00000260229.4	37	CCDS8319.1																																																																																			C|0.594;T|0.406	0.406	strong		0.438	MMP27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398128.1	NM_022122	
PANK1	53354	hgsc.bcm.edu	37	10	91371689	91371689	+	Silent	SNP	G	G	T	rs545008942		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr10:91371689G>T	ENST00000307534.4	-	2	975	c.820C>A	c.(820-822)Cgg>Agg	p.R274R	PANK1_ENST00000371774.2_Silent_p.R76R|PANK1_ENST00000342512.3_Silent_p.R49R|PANK1_ENST00000322191.6_Silent_p.R49R	NM_148977.2	NP_683878.1	Q8TE04	PANK1_HUMAN	pantothenate kinase 1	274					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						AAATACTTCCGGATGCTCTTC	0.483																																					p.R274R		Atlas-SNP	.											PANK1,NS,carcinoma,+1,1	PANK1	35	1	0			c.C820A						scavenged	.						113.0	103.0	106.0					10																	91371689		2203	4300	6503	SO:0001819	synonymous_variant	53354	exon2			ACTTCCGGATGCT	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.820C>A	10.37:g.91371689G>T		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	83	2	0.0240964	NM_148977	A6NIP0|Q7RTX6|Q7Z495|Q8TBQ8	Silent	SNP	ENST00000307534.4	37	CCDS31244.1																																																																																			.	.	none		0.483	PANK1-201	KNOWN	basic|CCDS	protein_coding	protein_coding			
OR13C5	138799	hgsc.bcm.edu	37	9	107361452	107361452	+	Silent	SNP	C	C	G	rs376107801|rs377523807|rs199665292	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr9:107361452C>G	ENST00000374779.2	-	1	336	c.243G>C	c.(241-243)acG>acC	p.T81T		NM_001004482.1	NP_001004482.1	Q8NGS8	O13C5_HUMAN	olfactory receptor, family 13, subfamily C, member 5	81						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(1)|large_intestine(2)|lung(11)|ovary(2)|pancreas(2)|prostate(2)|skin(4)	28						AGCTCACTAGCGTGGAGGGAA	0.512													G|||	1377	0.27496	0.3116	0.2133	5008	,	,		19807	0.4504		0.1163	False		,,,				2504	0.2515				p.T81T		Atlas-SNP	.											OR13C5,NS,carcinoma,-2,1	OR13C5	60	1	0			c.G243C						scavenged	.						15.0	28.0	23.0					9																	107361452		2059	4256	6315	SO:0001819	synonymous_variant	138799	exon1			CACTAGCGTGGAG		CCDS35091.1	9q31.1	2012-10-03			ENSG00000255800	ENSG00000277556		"""GPCR / Class A : Olfactory receptors"""	15100	protein-coding gene	gene with protein product							Standard	NM_001004482		Approved		uc011lvp.2	Q8NGS8	OTTHUMG00000020408	ENST00000374779.2:c.243G>C	9.37:g.107361452C>G		Somatic	677	5	0.00738552		WXS	Illumina HiSeq	Phase_I	608	9	0.0148026	NM_001004482	B2RNE5|B9EGW5|Q6IF53	Silent	SNP	ENST00000374779.2	37	CCDS35091.1																																																																																			.	.	weak		0.512	OR13C5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053479.2	NM_001004482	
CREBBP	1387	hgsc.bcm.edu	37	16	3789597	3789597	+	Missense_Mutation	SNP	C	C	A	rs200616542		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr16:3789597C>A	ENST00000262367.5	-	25	5071	c.4262G>T	c.(4261-4263)tGc>tTc	p.C1421F	CREBBP_ENST00000382070.3_Missense_Mutation_p.C1383F	NM_004380.2	NP_004371.2	Q92793	CBP_HUMAN	CREB binding protein	1421	CBP/p300-type HAT. {ECO:0000255|PROSITE- ProRule:PRU01065}.|Cys/His-rich.				cellular lipid metabolic process (GO:0044255)|cellular response to hypoxia (GO:0071456)|chromatin organization (GO:0006325)|embryonic digit morphogenesis (GO:0042733)|gene expression (GO:0010467)|germ-line stem cell maintenance (GO:0030718)|histone acetylation (GO:0016573)|homeostatic process (GO:0042592)|innate immune response (GO:0045087)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein complex assembly (GO:0006461)|regulation of smoothened signaling pathway (GO:0008589)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)|response to hypoxia (GO:0001666)|rhythmic process (GO:0048511)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nuclear body (GO:0016604)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	acetyltransferase activity (GO:0016407)|chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|histone acetyltransferase activity (GO:0004402)|MRF binding (GO:0043426)|p53 binding (GO:0002039)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II transcription coactivator activity (GO:0001105)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)	p.C1421Y(1)		NS(1)|breast(5)|central_nervous_system(4)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(125)|kidney(5)|large_intestine(32)|lung(43)|ovary(18)|pancreas(2)|prostate(6)|skin(9)|soft_tissue(1)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(21)	295		Ovarian(90;0.0266)		OV - Ovarian serous cystadenocarcinoma(1;3.54e-05)		TGGAGGGGGGCAATCAGAGCC	0.502			"""T, N, F, Mis, O"""	"""MLL, MORF, RUNXBP2"""	"""ALL, AML, DLBCL, B-NHL """		Rubinstein-Taybi syndrome																														p.C1421F		Atlas-SNP	.		Dom/Rec	yes		16	16p13.3	1387	CREB binding protein (CBP)	yes	L	CREBBP,NS,lymphoid_neoplasm,0,1	CREBBP	546	1	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.G4262T						scavenged	.						75.0	70.0	71.0					16																	3789597		2197	4300	6497	SO:0001583	missense	1387	exon25			GGGGGGCAATCAG	U85962	CCDS10509.1, CCDS45399.1	16p13.3	2011-07-01	2008-08-01		ENSG00000005339	ENSG00000005339		"""Chromatin-modifying enzymes / K-acetyltransferases"""	2348	protein-coding gene	gene with protein product		600140	"""Rubinstein-Taybi syndrome"""	RSTS		8413673	Standard	NM_001079846		Approved	RTS, CBP, KAT3A	uc002cvv.3	Q92793	OTTHUMG00000129431	ENST00000262367.5:c.4262G>T	16.37:g.3789597C>A	ENSP00000262367:p.Cys1421Phe	Somatic	74	1	0.0135135		WXS	Illumina HiSeq	Phase_I	76	45	0.592105	NM_004380	D3DUC9|O00147|Q16376|Q4LE28	Missense_Mutation	SNP	ENST00000262367.5	37	CCDS10509.1	.	.	.	.	.	.	.	.	.	.	c	19.94	3.920342	0.73098	.	.	ENSG00000005339	ENST00000262367;ENST00000543883;ENST00000382070;ENST00000323508	D;D	0.93133	-3.17;-3.17	5.36	5.36	0.76844	.	0.128977	0.56097	D	0.000038	D	0.97813	0.9282	H	0.94222	3.51	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.98507	1.0617	10	0.72032	D	0.01	-14.7453	19.4402	0.94817	0.0:1.0:0.0:0.0	.	1451;1421	Q4LE28;Q92793	.;CBP_HUMAN	F	1421;1451;1383;10	ENSP00000262367:C1421F;ENSP00000371502:C1383F	ENSP00000262367:C1421F	C	-	2	0	CREBBP	3729598	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	7.713000	0.84693	2.665000	0.90641	0.561000	0.74099	TGC	.	.	alt		0.502	CREBBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251591.2	NM_004380	
FCRLA	84824	hgsc.bcm.edu	37	1	161681780	161681780	+	Missense_Mutation	SNP	A	A	G	rs2275603	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr1:161681780A>G	ENST00000236938.6	+	4	849	c.607A>G	c.(607-609)Agc>Ggc	p.S203G	FCRLA_ENST00000367950.1_Intron|FCRLA_ENST00000470841.1_3'UTR|FCRLA_ENST00000367959.2_Missense_Mutation_p.S209G|FCRLA_ENST00000367949.2_Intron|FCRLA_ENST00000294796.4_Missense_Mutation_p.S52G|FCRLA_ENST00000309691.6_Missense_Mutation_p.S97G|FCRLA_ENST00000540521.1_Missense_Mutation_p.S69G|FCRLA_ENST00000349527.4_Intron|FCRLA_ENST00000540926.1_Missense_Mutation_p.S192G|FCRLA_ENST00000546024.1_Missense_Mutation_p.S114G|FCRLA_ENST00000367953.3_Missense_Mutation_p.S192G|FCRLA_ENST00000367957.2_Missense_Mutation_p.S63G|FCRLA_ENST00000350710.3_Intron	NM_032738.3	NP_116127.3	Q7L513	FCRLA_HUMAN	Fc receptor-like A	186	Ig-like C2-type 2.				cell differentiation (GO:0030154)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)				breast(1)|kidney(12)|large_intestine(4)|lung(13)|prostate(1)|skin(2)|stomach(1)	34	all_cancers(52;2.55e-15)|all_hematologic(112;0.0359)		BRCA - Breast invasive adenocarcinoma(70;0.00301)			CCAAGCAGGAAGCCCCATGAC	0.522													G|||	2389	0.477037	0.764	0.4553	5008	,	,		17754	0.5734		0.2078	False		,,,				2504	0.2822				p.S209G		Atlas-SNP	.											.	FCRLA	101	.	0			c.A625G						PASS	.	G	GLY/SER,GLY/SER,GLY/SER,,GLY/SER,,GLY/SER	2903,1503	477.0+/-357.8	980,943,280	116.0	145.0	135.0		625,340,205,,187,,607	-8.4	0.0	1	dbSNP_100	135	1882,6718	726.9+/-406.6	220,1442,2638	yes	missense,missense,missense,intron,missense,intron,missense	FCRLA	NM_001184866.1,NM_001184867.1,NM_001184870.1,NM_001184871.1,NM_001184872.1,NM_001184873.1,NM_032738.3	56,56,56,,56,,56	1200,2385,2918	GG,GA,AA		21.8837,34.1126,36.7907	benign,benign,benign,,benign,,benign	209/383,114/288,69/243,,63/237,,203/377	161681780	4785,8221	2203	4300	6503	SO:0001583	missense	84824	exon5			GCAGGAAGCCCCA	AF531423	CCDS30926.1, CCDS53415.1, CCDS53416.1, CCDS53417.1, CCDS53418.1, CCDS53419.1, CCDS53420.1	1q23.3	2014-01-28	2006-09-26	2006-09-26	ENSG00000132185	ENSG00000132185		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	18504	protein-coding gene	gene with protein product		606891	"""Fc receptor-like and mucin-like 1"""	FCRLM1		11754007	Standard	NM_001184866		Approved	MGC4595, FCRLc2, FCRLb, FCRLc1, FCRLd, FCRLe, FCRL, FCRLa, FREB, FCRLX	uc001gbe.3	Q7L513	OTTHUMG00000034537	ENST00000236938.6:c.607A>G	1.37:g.161681780A>G	ENSP00000236938:p.Ser203Gly	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	189	8	0.042328	NM_001184866	A0N0M1|A6NC03|A6NL20|F5H720|F8W743|G3V1J2|Q5VXA1|Q5VXA2|Q5VXA3|Q5VXA4|Q5VXB0|Q5VXB1|Q8NEW4|Q8WXH3|Q96PC6|Q96PJ0|Q96PJ1|Q96PJ2|Q96PJ4|Q9BR57	Missense_Mutation	SNP	ENST00000236938.6	37	CCDS30926.1	977	0.44734432234432236	357	0.725609756097561	143	0.39502762430939226	317	0.5541958041958042	160	0.21108179419525067	G	0.009	-1.843804	0.00568	0.658874	0.218837	ENSG00000132185	ENST00000236938;ENST00000367959;ENST00000546024;ENST00000540521;ENST00000540926;ENST00000367957;ENST00000309691;ENST00000294796;ENST00000367953	T;T;T;T;T;T;T;T;T	0.11495	2.77;2.77;2.77;2.77;2.77;2.77;2.77;2.77;2.77	5.57	-8.4	0.00965	.	0.922351	0.09125	N	0.845187	T	0.02610	0.0079	L	0.41356	1.27	0.80722	P	0.0	B;B;B;B;B	0.06786	0.0;0.001;0.0;0.0;0.0	B;B;B;B;B	0.15484	0.001;0.013;0.001;0.0;0.001	T	0.46105	-0.9215	9	0.08837	T	0.75	.	20.1836	0.98210	0.8865:0.0:0.1135:0.0	rs2275603;rs60711230;rs2275603	69;63;114;209;203	F5H720;Q5VXB1;G3V1J2;A6NC03;Q7L513-9	.;.;.;.;.	G	203;209;114;69;192;63;97;52;192	ENSP00000236938:S203G;ENSP00000356936:S209G;ENSP00000439838:S114G;ENSP00000442870:S69G;ENSP00000446380:S192G;ENSP00000356934:S63G;ENSP00000309596:S97G;ENSP00000294796:S52G;ENSP00000356930:S192G	ENSP00000236938:S203G	S	+	1	0	FCRLA	159948404	0.000000	0.05858	0.000000	0.03702	0.054000	0.15201	-0.373000	0.07494	-2.199000	0.00748	-0.930000	0.02707	AGC	A|0.595;G|0.405	0.405	strong		0.522	FCRLA-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083574.1	NM_032738	
FOXD4	2298	hgsc.bcm.edu	37	9	117998	117998	+	Missense_Mutation	SNP	G	G	T	rs66612967	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr9:117998G>T	ENST00000382500.2	-	1	419	c.122C>A	c.(121-123)gCg>gAg	p.A41E		NM_207305.4	NP_997188.2	Q12950	FOXD4_HUMAN	forkhead box D4	41					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding, bending (GO:0008301)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.A41E(1)		endometrium(5)|large_intestine(2)|lung(3)|prostate(1)|skin(3)	14	all_lung(41;0.218)	all_cancers(5;0.0395)|Acute lymphoblastic leukemia(5;1.91e-07)|all_hematologic(5;1.95e-06)	Kidney(42;0.112)|KIRC - Kidney renal clear cell carcinoma(5;0.157)	all cancers(5;0.000704)|Lung(218;0.00755)|GBM - Glioblastoma multiforme(5;0.0149)|Epithelial(6;0.0154)		CTGGCTCGCCGCCTCCTCCTC	0.682													T|||	111	0.0221645	0.0749	0.013	5008	,	,		13954	0.001		0.002	False		,,,				2504	0.0				p.A41E		Atlas-SNP	.											FOXD4_ENST00000382500,NS,carcinoma,0,3	FOXD4	75	3	1	Substitution - Missense(1)	skin(1)	c.C122A						scavenged	.						38.0	53.0	48.0					9																	117998		2203	4298	6501	SO:0001583	missense	2298	exon1			CTCGCCGCCTCCT	U13223	CCDS34975.1	9p24.3	2014-09-17			ENSG00000170122	ENSG00000170122		"""Forkhead boxes"""	3805	protein-coding gene	gene with protein product		601092		FKHL9		7957066, 8825632, 12234674	Standard	NM_207305		Approved	FREAC5, FOXD4a	uc003zfz.4	Q12950	OTTHUMG00000021015	ENST00000382500.2:c.122C>A	9.37:g.117998G>T	ENSP00000371940:p.Ala41Glu	Somatic	328	14	0.0426829		WXS	Illumina HiSeq	Phase_I	371	29	0.0781671	NM_207305	B2RN05|B9EGL7|Q5VVK1|Q8WXT6	Missense_Mutation	SNP	ENST00000382500.2	37	CCDS34975.1	50	0.022893772893772892	43	0.08739837398373984	4	0.011049723756906077	3	0.005244755244755245	0	0.0	.	0.012	-1.673624	0.00758	.	.	ENSG00000170122	ENST00000382500	D	0.94457	-3.43	1.56	1.56	0.23342	.	.	.	.	.	T	0.13030	0.0316	N	0.01352	-0.895	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.57458	-0.7808	9	0.02654	T	1	.	4.5559	0.12136	0.0:0.0:0.3427:0.6573	.	41	Q12950	FOXD4_HUMAN	E	41	ENSP00000371940:A41E	ENSP00000371940:A41E	A	-	2	0	FOXD4	107998	0.001000	0.12720	0.001000	0.08648	0.003000	0.03518	-0.379000	0.07437	0.095000	0.17434	-1.316000	0.01300	GCG	G|0.977;T|0.023	0.023	strong		0.682	FOXD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055433.1	NM_207305	
NOX4	50507	hgsc.bcm.edu	37	11	89060002	89060002	+	Silent	SNP	G	G	A	rs28517716	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr11:89060002G>A	ENST00000263317.4	-	18	1897	c.1659C>T	c.(1657-1659)tcC>tcT	p.S553S	NOX4_ENST00000535633.1_Silent_p.S529S|NOX4_ENST00000542487.1_Silent_p.S529S|NOX4_ENST00000343727.5_Silent_p.S529S|NOX4_ENST00000531342.1_Silent_p.S206S|NOX4_ENST00000527626.1_Silent_p.S366S|NOX4_ENST00000532825.1_Silent_p.S489S|NOX4_ENST00000413594.2_Silent_p.S574S|NOX4_ENST00000375979.3_Silent_p.S246S|NOX4_ENST00000525196.1_Silent_p.S317S|NOX4_ENST00000527956.1_Silent_p.S529S|NOX4_ENST00000534731.1_Silent_p.S513S|NOX4_ENST00000424319.1_Silent_p.S529S|NOX4_ENST00000528341.1_Silent_p.S528S			Q9NPH5	NOX4_HUMAN	NADPH oxidase 4	553	Mediates interaction with TLR4.				bone resorption (GO:0045453)|cardiac muscle cell differentiation (GO:0055007)|cell aging (GO:0007569)|cell morphogenesis (GO:0000902)|cellular response to cAMP (GO:0071320)|cellular response to gamma radiation (GO:0071480)|cellular response to glucose stimulus (GO:0071333)|cellular response to transforming growth factor beta stimulus (GO:0071560)|homocysteine metabolic process (GO:0050667)|inflammatory response (GO:0006954)|negative regulation of cell proliferation (GO:0008285)|oxidation-reduction process (GO:0055114)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of smooth muscle cell migration (GO:0014911)|positive regulation of stress fiber assembly (GO:0051496)|reactive oxygen species metabolic process (GO:0072593)|response to hypoxia (GO:0001666)|superoxide anion generation (GO:0042554)	apical plasma membrane (GO:0016324)|endoplasmic reticulum (GO:0005783)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|NADPH oxidase complex (GO:0043020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|heme binding (GO:0020037)|modified amino acid binding (GO:0072341)|NAD(P)H oxidase activity (GO:0016174)|nucleotide binding (GO:0000166)|oxygen sensor activity (GO:0019826)|superoxide-generating NADPH oxidase activity (GO:0016175)			NS(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(8)|lung(20)|ovary(2)|prostate(3)|skin(2)	44		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.011)				GAAGAGTCTTGGATAGTGAAT	0.368													G|||	660	0.131789	0.2405	0.0418	5008	,	,		16825	0.1429		0.0507	False		,,,				2504	0.1207				p.S553S		Atlas-SNP	.											NOX4,NS,carcinoma,-1,1	NOX4	101	1	0			c.C1659T						scavenged	.	G	,,	791,3611	299.6+/-285.9	68,655,1478	89.0	89.0	89.0		1539,1587,1659	2.4	1.0	11	dbSNP_125	89	347,8251	115.5+/-175.4	5,337,3957	no	coding-synonymous,coding-synonymous,coding-synonymous	NOX4	NM_001143836.1,NM_001143837.1,NM_016931.3	,,	73,992,5435	AA,AG,GG		4.0358,17.9691,8.7538	,,	513/539,529/555,553/579	89060002	1138,11862	2201	4299	6500	SO:0001819	synonymous_variant	50507	exon18			AGTCTTGGATAGT	AF254621	CCDS8285.1, CCDS44695.1, CCDS44696.1, CCDS73361.1, CCDS73362.1	11q14.2-q21	2008-02-05			ENSG00000086991	ENSG00000086991			7891	protein-coding gene	gene with protein product		605261					Standard	NM_001143837		Approved	KOX-1, KOX	uc001pct.3	Q9NPH5	OTTHUMG00000167298	ENST00000263317.4:c.1659C>T	11.37:g.89060002G>A		Somatic	217	2	0.00921659		WXS	Illumina HiSeq	Phase_I	222	5	0.0225225	NM_016931	A8K715|B7Z520|E7EMD7|Q5K3R4|Q5K3R5|Q5K3R6|Q5K3R8|Q7Z7G3|Q86V92	Silent	SNP	ENST00000263317.4	37	CCDS8285.1																																																																																			G|0.912;A|0.088	0.088	strong		0.368	NOX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394054.1	NM_016931	
ZNF879	345462	hgsc.bcm.edu	37	5	178459283	178459283	+	Missense_Mutation	SNP	A	A	G	rs17078988	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr5:178459283A>G	ENST00000444149.2	+	5	522	c.334A>G	c.(334-336)Aca>Gca	p.T112A	ZNF879_ENST00000519896.1_3'UTR	NM_001136116.1	NP_001129588.1	B4DU55	ZN879_HUMAN	zinc finger protein 879	112					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(3)|kidney(2)|pancreas(1)|stomach(1)	7						AATTGATGGCACATTTGACTT	0.333													G|||	1824	0.364217	0.5182	0.255	5008	,	,		18690	0.4276		0.2237	False		,,,				2504	0.3129				p.T112A		Atlas-SNP	.											.	ZNF879	41	.	0			c.A334G						PASS	.	G	ALA/THR	618,766		138,342,212	98.0	83.0	87.0		334	-2.4	0.0	5	dbSNP_123	87	706,2476		76,554,961	yes	missense	ZNF879	NM_001136116.1	58	214,896,1173	GG,GA,AA		22.1873,44.6532,28.9969	benign	112/564	178459283	1324,3242	692	1591	2283	SO:0001583	missense	345462	exon5			GATGGCACATTTG	AK300504	CCDS47352.1	5q35.3	2013-01-08			ENSG00000234284	ENSG00000234284		"""Zinc fingers, C2H2-type"", ""-"""	37273	protein-coding gene	gene with protein product							Standard	NM_001136116		Approved	DKFZp686E2433	uc003mjt.4	B4DU55	OTTHUMG00000163596	ENST00000444149.2:c.334A>G	5.37:g.178459283A>G	ENSP00000414887:p.Thr112Ala	Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	187	8	0.0427807	NM_001136116		Missense_Mutation	SNP	ENST00000444149.2	37	CCDS47352.1	768	0.3516483516483517	243	0.49390243902439024	100	0.27624309392265195	244	0.42657342657342656	181	0.23878627968337732	G	0	-2.590623	0.00126	0.446532	0.221873	ENSG00000234284	ENST00000444149;ENST00000522442	T;T	0.06142	3.34;5.87	4.32	-2.37	0.06643	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.42137	-0.9469	8	0.07030	T	0.85	0.427	1.2422	0.01965	0.3576:0.2448:0.2425:0.1551	rs17078988;rs52795425;rs17078988	112	B4DU55	ZN879_HUMAN	A	112	ENSP00000414887:T112A;ENSP00000428477:T112A	ENSP00000414887:T112A	T	+	1	0	ZNF879	178391889	0.000000	0.05858	0.000000	0.03702	0.019000	0.09904	-2.139000	0.01302	-1.063000	0.03177	-4.156000	0.00010	ACA	A|0.634;G|0.366	0.366	strong		0.333	ZNF879-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374447.1	NM_001136116	
TNXB	7148	hgsc.bcm.edu	37	6	32010272	32010272	+	Missense_Mutation	SNP	T	T	A	rs17421133	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr6:32010272T>A	ENST00000375244.3	-	40	12371	c.12170A>T	c.(12169-12171)aAc>aTc	p.N4057I	TNXB_ENST00000451343.1_Missense_Mutation_p.N486I|TNXB_ENST00000375247.2_Missense_Mutation_p.N4055I			P22105	TENX_HUMAN	tenascin XB	4102	Fibronectin type-III 32. {ECO:0000255|PROSITE-ProRule:PRU00316}.				actin cytoskeleton organization (GO:0030036)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|collagen fibril organization (GO:0030199)|collagen metabolic process (GO:0032963)|elastic fiber assembly (GO:0048251)|extracellular fibril organization (GO:0043206)|fatty acid metabolic process (GO:0006631)|regulation of JUN kinase activity (GO:0043506)|single organismal cell-cell adhesion (GO:0016337)|triglyceride metabolic process (GO:0006641)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|integrin binding (GO:0005178)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)	8						GCAAAACACGTTCAGGGGCCG	0.667													T|||	1087	0.217053	0.0212	0.3761	5008	,	,		19961	0.2202		0.34	False		,,,				2504	0.2393				p.N4055I		Atlas-SNP	.											TNXB_ENST00000375247,colon,carcinoma,0,3	TNXB	553	3	0			c.A12164T						scavenged	.	T	ILE/ASN,ILE/ASN	228,2794		17,194,1300	52.0	46.0	48.0		12164,1457	3.3	0.8	6	dbSNP_131	48	1707,3711		266,1175,1268	no	missense,missense	TNXB	NM_019105.6,NM_032470.3	149,149	283,1369,2568	AA,AT,TT		31.5061,7.5447,22.9265	possibly-damaging,possibly-damaging	4055/4243,486/674	32010272	1935,6505	1511	2709	4220	SO:0001583	missense	7148	exon40			AACACGTTCAGGG	X71923	CCDS4736.1	6p21.3	2013-02-11			ENSG00000168477	ENSG00000168477		"""Fibrinogen C domain containing"", ""Fibronectin type III domain containing"""	11976	protein-coding gene	gene with protein product		600985		TNXB1, TNXB2		8530023	Standard	NM_019105		Approved	TNXBS, XBS, XB	uc021yvf.2	P22105	OTTHUMG00000031088	ENST00000375244.3:c.12170A>T	6.37:g.32010272T>A	ENSP00000364393:p.Asn4057Ile	Somatic	273	0	0		WXS	Illumina HiSeq	Phase_I	306	4	0.0130719	NM_019105	P78530|P78531|Q08424|Q08AM0|Q08AM1|Q59GU7|Q5SQD3|Q5ST74|Q7L8Q4|Q8N4R1|Q9NPK9|Q9UC10|Q9UC11|Q9UC12|Q9UC13|Q9UMG7	Missense_Mutation	SNP	ENST00000375244.3	37		566	0.2591575091575092	17	0.034552845528455285	146	0.40331491712707185	132	0.23076923076923078	271	0.3575197889182058	t	14.60	2.582663	0.46006	0.075447	0.315061	ENSG00000168477	ENST00000375244;ENST00000451343;ENST00000375247	T;T;T	0.77229	-1.08;-1.08;-1.08	4.45	3.29	0.37713	.	0.834350	0.10489	N	0.668630	T	0.65933	0.2739	L	0.37561	1.115	0.80722	P	0.0	D	0.61080	0.989	P	0.57371	0.819	T	0.59804	-0.7385	9	0.54805	T	0.06	.	4.5535	0.12126	0.1704:0.0936:0.0:0.736	rs17421133;rs28361046;rs17421133	4055	P22105-3	.	I	4057;486;4055	ENSP00000364393:N4057I;ENSP00000407685:N486I;ENSP00000364396:N4055I	ENSP00000364393:N4057I	N	-	2	0	TNXB	32118251	0.000000	0.05858	0.797000	0.32132	0.994000	0.84299	0.054000	0.14205	0.764000	0.33197	0.456000	0.33151	AAC	T|0.754;A|0.246	0.246	strong		0.667	TNXB-001	PUTATIVE	not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000268927.2	NM_019105	
OR3A3	8392	hgsc.bcm.edu	37	17	3324810	3324810	+	Missense_Mutation	SNP	A	A	G	rs227787	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr17:3324810A>G	ENST00000291231.1	+	1	949	c.949A>G	c.(949-951)Aag>Gag	p.K317E		NM_012373.2	NP_036505.2	P47888	OR3A3_HUMAN	olfactory receptor, family 3, subfamily A, member 3	317			K -> E (in dbSNP:rs227787). {ECO:0000269|PubMed:10673334, ECO:0000269|PubMed:14983052, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.2, ECO:0000269|Ref.3, ECO:0000269|Ref.4}.		signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(3)|prostate(1)	9						ACTTGTGGGGAAGCGATCACT	0.468													A|||	1723	0.34405	0.2337	0.4121	5008	,	,		19096	0.3819		0.2445	False		,,,				2504	0.5082				p.K317E		Atlas-SNP	.											.	OR3A3	20	.	0			c.A949G						PASS	.	A	GLU/LYS	1071,3335		137,797,1269	73.0	74.0	74.0		949	2.0	0.0	17	dbSNP_79	74	1915,6685		238,1439,2623	yes	missense	OR3A3	NM_012373.2	56	375,2236,3892	GG,GA,AA		22.2674,24.3078,22.9586	benign	317/322	3324810	2986,10020	2203	4300	6503	SO:0001583	missense	8392	exon1			GTGGGGAAGCGAT	U04688	CCDS11025.1	17p13.3	2012-08-09			ENSG00000159961	ENSG00000159961		"""GPCR / Class A : Olfactory receptors"""	8284	protein-coding gene	gene with protein product				OR3A6, OR3A7, OR3A8P		8004088, 9500546	Standard	NM_012373		Approved	OR17-201, OR17-137, OR17-16	uc010vrd.2	P47888	OTTHUMG00000090649	ENST00000291231.1:c.949A>G	17.37:g.3324810A>G	ENSP00000291231:p.Lys317Glu	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	73	4	0.0547945	NM_012373	Q2VPE4|Q6IFM6|Q9P1Q4|Q9UBE7	Missense_Mutation	SNP	ENST00000291231.1	37	CCDS11025.1	646	0.2957875457875458	122	0.24796747967479674	125	0.3453038674033149	221	0.38636363636363635	178	0.23482849604221637	.	9.673	1.147227	0.21288	0.243078	0.222674	ENSG00000159961	ENST00000291231	T	0.39406	1.08	3.09	2.01	0.26516	.	.	.	.	.	T	0.00012	0.0000	N	0.25245	0.725	0.80722	P	0.0	B	0.12013	0.005	B	0.14023	0.01	T	0.40534	-0.9558	8	0.59425	D	0.04	.	4.3978	0.11372	0.8427:0.0:0.1573:0.0	rs227787;rs230391;rs391407;rs56498918;rs60332366;rs227787	317	P47888	OR3A3_HUMAN	E	317	ENSP00000291231:K317E	ENSP00000291231:K317E	K	+	1	0	OR3A3	3271560	0.007000	0.16637	0.001000	0.08648	0.021000	0.10359	1.921000	0.40035	1.387000	0.46486	0.533000	0.62120	AAG	G|0.262;N|0.001	0.262	strong		0.468	OR3A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207309.1		
KIF13A	63971	hgsc.bcm.edu	37	6	17831419	17831419	+	Silent	SNP	G	G	A	rs2277080	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr6:17831419G>A	ENST00000259711.6	-	13	1419	c.1314C>T	c.(1312-1314)tcC>tcT	p.S438S	KIF13A_ENST00000378843.2_Silent_p.S438S|KIF13A_ENST00000378816.5_Silent_p.S438S|KIF13A_ENST00000378826.2_Silent_p.S438S|KIF13A_ENST00000378814.5_Silent_p.S438S	NM_022113.5	NP_071396.4	Q9H1H9	KI13A_HUMAN	kinesin family member 13A	438					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)			CCTTGATACCGGACATCTCCA	0.408													G|||	1199	0.239417	0.1566	0.1758	5008	,	,		22334	0.2004		0.2803	False		,,,				2504	0.3947				p.S438S		Atlas-SNP	.											.	KIF13A	276	.	0			c.C1314T						PASS	.	G	,,,	645,3153		59,527,1313	124.0	121.0	122.0		1314,1314,1314,1314	-7.8	0.2	6	dbSNP_100	122	2399,5857		341,1717,2070	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	KIF13A	NM_001105566.2,NM_001105567.2,NM_001105568.2,NM_022113.5	,,,	400,2244,3383	AA,AG,GG		29.0577,16.9826,25.253	,,,	438/1771,438/1758,438/1750,438/1806	17831419	3044,9010	1899	4128	6027	SO:0001819	synonymous_variant	63971	exon13			GATACCGGACATC	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.1314C>T	6.37:g.17831419G>A		Somatic	190	0	0		WXS	Illumina HiSeq	Phase_I	140	8	0.0571429	NM_001105567	A0JP21|A0JP22|F2Z382|Q5THQ2|Q5THQ3|Q9H193|Q9H194|Q9H1H8	Silent	SNP	ENST00000259711.6	37	CCDS47381.1																																																																																			G|0.777;A|0.223	0.223	strong		0.408	KIF13A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039954.4		
URB2	9816	hgsc.bcm.edu	37	1	229772932	229772932	+	Missense_Mutation	SNP	A	A	G	rs3811474	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr1:229772932A>G	ENST00000258243.2	+	4	2708	c.2572A>G	c.(2572-2574)Aaa>Gaa	p.K858E		NM_014777.2	NP_055592.2	Q14146	URB2_HUMAN	URB2 ribosome biogenesis 2 homolog (S. cerevisiae)	858						aggresome (GO:0016235)|nucleolus (GO:0005730)|nucleus (GO:0005634)				breast(1)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(33)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(6)	73						CAGATTTGCAAAAGCTGGACC	0.502													A|||	998	0.199281	0.1952	0.2421	5008	,	,		20179	0.4315		0.0636	False		,,,				2504	0.0746				p.K858E		Atlas-SNP	.											.	URB2	152	.	0			c.A2572G						PASS	.	A	GLU/LYS	844,3562	332.5+/-302.5	85,674,1444	86.0	90.0	89.0		2572	2.6	0.0	1	dbSNP_107	89	553,8047	150.6+/-205.5	14,525,3761	yes	missense	URB2	NM_014777.2	56	99,1199,5205	GG,GA,AA		6.4302,19.1557,10.7412	possibly-damaging	858/1525	229772932	1397,11609	2203	4300	6503	SO:0001583	missense	9816	exon4			TTTGCAAAAGCTG	D50923	CCDS31052.1	1q42.13	2009-11-06	2008-10-01	2008-10-01	ENSG00000135763	ENSG00000135763			28967	protein-coding gene	gene with protein product	"""nucleolar preribosomal-associated protein 1"""		"""KIAA0133"""	KIAA0133		8590280	Standard	NM_014777		Approved	NPA2, NET10	uc001hts.1	Q14146	OTTHUMG00000039464	ENST00000258243.2:c.2572A>G	1.37:g.229772932A>G	ENSP00000258243:p.Lys858Glu	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	100	8	0.08	NM_014777	Q5VYC9	Missense_Mutation	SNP	ENST00000258243.2	37	CCDS31052.1	489	0.2239010989010989	99	0.20121951219512196	75	0.20718232044198895	271	0.4737762237762238	44	0.05804749340369393	A	7.495	0.651409	0.14516	0.191557	0.064302	ENSG00000135763	ENST00000258243	T	0.30182	1.54	4.95	2.59	0.31030	.	0.631054	0.17336	N	0.177928	T	0.00012	0.0000	L	0.29908	0.895	0.80722	P	0.0	B	0.21381	0.055	B	0.20955	0.032	T	0.47249	-0.9132	8	.	.	.	-2.8656	2.4527	0.04522	0.6029:0.1342:0.1332:0.1297	rs3811474;rs61291674;rs3811474	858	Q14146	URB2_HUMAN	E	858	ENSP00000258243:K858E	.	K	+	1	0	URB2	227839555	0.017000	0.18338	0.001000	0.08648	0.505000	0.33919	2.475000	0.45162	0.831000	0.34780	0.477000	0.44152	AAA	A|0.836;G|0.164	0.164	strong		0.502	URB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095232.1	NM_014777	
BHLHB9	80823	hgsc.bcm.edu	37	X	102004884	102004884	+	Missense_Mutation	SNP	G	G	T			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chrX:102004884G>T	ENST00000372735.1	+	4	1546	c.961G>T	c.(961-963)Gat>Tat	p.D321Y	BHLHB9_ENST00000447531.1_Missense_Mutation_p.D321Y|BHLHB9_ENST00000448867.1_Missense_Mutation_p.D321Y|BHLHB9_ENST00000361229.4_Missense_Mutation_p.D321Y|BHLHB9_ENST00000457056.1_Missense_Mutation_p.D321Y			Q6PI77	BHLH9_HUMAN	basic helix-loop-helix domain containing, class B, 9	321					learning or memory (GO:0007611)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of neurogenesis (GO:0050769)|positive regulation of synapse assembly (GO:0051965)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	protein homodimerization activity (GO:0042803)			cervix(1)|endometrium(6)|kidney(3)|large_intestine(1)|lung(8)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	26						ATGCTATATGGATTCTGAGGA	0.383																																					p.D321Y		Atlas-SNP	.											.	BHLHB9	60	.	0			c.G961T						PASS	.						83.0	79.0	80.0					X																	102004884		2203	4300	6503	SO:0001583	missense	80823	exon2			TATATGGATTCTG	AB051488	CCDS14502.1	Xq23	2014-03-21			ENSG00000198908	ENSG00000198908		"""Basic helix-loop-helix proteins"", ""Armadillo repeat containing"""	29353	protein-coding gene	gene with protein product		300921				11214970, 15034937, 16221301	Standard	NM_030639		Approved	p60TRP, KIAA1701, GASP3	uc011mrv.2	Q6PI77	OTTHUMG00000022060	ENST00000372735.1:c.961G>T	X.37:g.102004884G>T	ENSP00000361820:p.Asp321Tyr	Somatic	179	0	0		WXS	Illumina HiSeq	Phase_I	154	38	0.246753	NM_001142530	Q9C0G2	Missense_Mutation	SNP	ENST00000372735.1	37	CCDS14502.1	.	.	.	.	.	.	.	.	.	.	G	11.02	1.516286	0.27123	.	.	ENSG00000198908	ENST00000457056;ENST00000361229;ENST00000447531;ENST00000448867;ENST00000372735	T;T;T;T;T	0.33438	1.41;1.41;1.41;1.41;1.41	4.6	0.444	0.16592	Armadillo-type fold (1);	0.425883	0.20121	N	0.098805	T	0.28532	0.0706	L	0.38175	1.15	0.21445	N	0.999684	P	0.43231	0.801	P	0.49999	0.628	T	0.11421	-1.0588	9	.	.	.	-7.4256	6.7343	0.23401	0.5217:0.0:0.4783:0.0	.	321	Q6PI77	BHLH9_HUMAN	Y	321	ENSP00000403226:D321Y;ENSP00000354675:D321Y;ENSP00000405893:D321Y;ENSP00000391722:D321Y;ENSP00000361820:D321Y	.	D	+	1	0	BHLHB9	101891540	0.980000	0.34600	0.331000	0.25455	0.649000	0.38597	0.014000	0.13333	-0.059000	0.13154	-0.269000	0.10298	GAT	.	.	none		0.383	BHLHB9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057630.1	NM_030639	
SLC2A9	56606	hgsc.bcm.edu	37	4	9998493	9998493	+	Silent	SNP	A	A	G	rs13113918	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr4:9998493A>G	ENST00000264784.3	-	3	375	c.322T>C	c.(322-324)Ttg>Ctg	p.L108L	SLC2A9_ENST00000506583.1_Silent_p.L79L|SLC2A9_ENST00000309065.3_Silent_p.L79L	NM_020041.2	NP_064425.2	Q9NRM0	GTR9_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 9	108					glucose transport (GO:0015758)|proton transport (GO:0015992)|transmembrane transport (GO:0055085)|urate metabolic process (GO:0046415)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)	glucose transmembrane transporter activity (GO:0005355)|sugar:proton symporter activity (GO:0005351)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(12)|ovary(3)|pancreas(1)|prostate(2)|skin(4)|stomach(1)	35					Losartan(DB00678)|Probenecid(DB01032)	GACCAGAGCAAAGTCAGAGTG	0.448													G|||	4110	0.820687	0.7784	0.7219	5008	,	,		20309	0.9722		0.8002	False		,,,				2504	0.8129				p.L108L		Atlas-SNP	.											.	SLC2A9	158	.	0			c.T322C						PASS	.	G	,	3421,985	369.3+/-319.0	1329,763,111	155.0	134.0	141.0		235,322	5.2	0.9	4	dbSNP_121	141	6754,1846	330.6+/-319.3	2651,1452,197	no	coding-synonymous,coding-synonymous	SLC2A9	NM_001001290.1,NM_020041.2	,	3980,2215,308	GG,GA,AA		21.4651,22.3559,21.7669	,	79/512,108/541	9998493	10175,2831	2203	4300	6503	SO:0001819	synonymous_variant	56606	exon3			AGAGCAAAGTCAG	AF210317	CCDS3406.1, CCDS3407.1	4p16.1	2013-05-22			ENSG00000109667	ENSG00000109667		"""Solute carriers"""	13446	protein-coding gene	gene with protein product	"""urate voltage-driven efflux transporter 1"""	606142				10860667, 17710649	Standard	NM_020041		Approved	Glut9, GLUTX, URATv1	uc003gmc.3	Q9NRM0	OTTHUMG00000044263	ENST00000264784.3:c.322T>C	4.37:g.9998493A>G		Somatic	193	0	0		WXS	Illumina HiSeq	Phase_I	196	9	0.0459184	NM_020041	Q0VGC4|Q4W5D1|Q8WV30|Q96P00	Silent	SNP	ENST00000264784.3	37	CCDS3407.1																																																																																			A|0.196;G|0.804	0.804	strong		0.448	SLC2A9-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207055.1		
XAF1	54739	hgsc.bcm.edu	37	17	6663895	6663895	+	Silent	SNP	C	C	G	rs2271231|rs386794960	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr17:6663895C>G	ENST00000361842.3	+	4	635	c.396C>G	c.(394-396)cgC>cgG	p.R132R	XAF1_ENST00000346752.4_Silent_p.R113R|XAF1_ENST00000438512.1_Silent_p.R132R|XAF1_ENST00000441631.1_Silent_p.R132R	NM_017523.3	NP_059993.2	Q6GPH4	XAF1_HUMAN	XIAP associated factor 1	132			R -> H (in dbSNP:rs2271232).	R -> Q (in Ref. 3; BAF85537). {ECO:0000305}.	apoptotic process (GO:0006915)|cytokine-mediated signaling pathway (GO:0019221)|negative regulation of protein complex assembly (GO:0031333)|response to interferon-beta (GO:0035456)|type I interferon signaling pathway (GO:0060337)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			large_intestine(2)|lung(2)|prostate(1)|urinary_tract(1)	6						ATGTCTGTCGCAGTGAACAGG	0.592													G|||	2629	0.52496	0.7383	0.3934	5008	,	,		17143	0.5813		0.3141	False		,,,				2504	0.4888				p.R132R		Atlas-SNP	.											XAF1,colon,carcinoma,+2,1	XAF1	16	1	0			c.C396G						scavenged	.	G	,	2694,1712		958,778,467	51.0	50.0	50.0		396,339	1.8	0.0	17	dbSNP_100	50	2637,5963		446,1745,2109	no	coding-synonymous,coding-synonymous	XAF1	NM_017523.2,NM_199139.1	,	1404,2523,2576	GG,GC,CC		30.6628,38.8561,40.9888	,	132/302,113/283	6663895	5331,7675	2203	4300	6503	SO:0001819	synonymous_variant	54739	exon4			CTGTCGCAGTGAA	X99699	CCDS11080.1, CCDS11081.1	17p13.2	2010-03-19			ENSG00000132530	ENSG00000132530			30932	protein-coding gene	gene with protein product		606717				12029096, 11175744	Standard	NM_199139		Approved	BIRC4BP, XIAPAF1, HSXIAPAF1	uc002gdn.3	Q6GPH4		ENST00000361842.3:c.396C>G	17.37:g.6663895C>G		Somatic	221	1	0.00452489		WXS	Illumina HiSeq	Phase_I	203	7	0.0344828	NM_017523	A2T931|A2T932|A8K2L1|A8K9Y3|D3DTM6|Q6MZE8|Q8N557|Q99982	Silent	SNP	ENST00000361842.3	37	CCDS11080.1																																																																																			C|0.550;G|0.450	0.450	strong		0.592	XAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439643.5	NM_017523	
TAS2R43	259289	hgsc.bcm.edu	37	12	11244166	11244166	+	Silent	SNP	G	G	C	rs35720106	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr12:11244166G>C	ENST00000531678.1	-	1	746	c.663C>G	c.(661-663)acC>acG	p.T221T	PRR4_ENST00000536668.1_Intron|TAS2R14_ENST00000381852.4_Intron	NM_176884.2	NP_795365.2	P59537	T2R43_HUMAN	taste receptor, type 2, member 43	221					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|G-protein coupled receptor signaling pathway (GO:0007186)	integral component of membrane (GO:0016021)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)|taste receptor activity (GO:0008527)	p.T221T(1)		endometrium(1)|ovary(1)|prostate(2)|urinary_tract(1)	5			OV - Ovarian serous cystadenocarcinoma(49;0.0344)	BRCA - Breast invasive adenocarcinoma(232;0.196)		TGTGGACCTTGGTGCTGGGAT	0.398													.|||	3199	0.638778	0.1218	0.7205	5008	,	,		13366	0.9405		0.7793	False		,,,				2504	0.8241				p.T221T		Atlas-SNP	.											TAS2R43,NS,carcinoma,0,2	TAS2R43	19	2	1	Substitution - coding silent(1)	prostate(1)	c.C663G						PASS	.						130.0	112.0	118.0					12																	11244166		2176	4249	6425	SO:0001819	synonymous_variant	259289	exon1			GACCTTGGTGCTG	AF494237	CCDS53749.1	12p13.2	2012-08-22				ENSG00000255374		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	18875	protein-coding gene	gene with protein product		612668				12379855	Standard	NM_176884		Approved	T2R52	uc001qzq.1	P59537		ENST00000531678.1:c.663C>G	12.37:g.11244166G>C		Somatic	20	0	0		WXS	Illumina HiSeq	Phase_I	31	14	0.451613	NM_176884	P59546|Q645X4	Silent	SNP	ENST00000531678.1	37	CCDS53749.1																																																																																			G|0.614;C|0.386	0.386	strong		0.398	TAS2R43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383561.1	NM_176884	
ADAM23	8745	hgsc.bcm.edu	37	2	207425911	207425911	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr2:207425911G>A	ENST00000264377.3	+	12	1557	c.1229G>A	c.(1228-1230)cGc>cAc	p.R410H	ADAM23_ENST00000374415.3_Missense_Mutation_p.R410H|ADAM23_ENST00000374416.1_Missense_Mutation_p.R410H	NM_003812.2	NP_003803.1	O75077	ADA23_HUMAN	ADAM metallopeptidase domain 23	410	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				cell adhesion (GO:0007155)|central nervous system development (GO:0007417)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.R410H(2)		NS(2)|breast(1)|endometrium(6)|kidney(3)|large_intestine(5)|liver(2)|lung(22)|ovary(2)|prostate(3)|skin(3)|stomach(1)|urinary_tract(1)	51				LUSC - Lung squamous cell carcinoma(261;0.0961)|Lung(261;0.182)|Epithelial(149;0.205)		GTCTGTTCTCGCACAAGAGGA	0.413																																					p.R410H	Melanoma(194;1127 2130 19620 24042 27855)	Atlas-SNP	.											ADAM23_ENST00000374416,NS,carcinoma,0,2	ADAM23	239	2	2	Substitution - Missense(2)	prostate(2)	c.G1229A						PASS	.						155.0	160.0	158.0					2																	207425911		2203	4300	6503	SO:0001583	missense	8745	exon12			GTTCTCGCACAAG	AB009672	CCDS2369.1	2q33	2008-06-12	2005-08-18		ENSG00000114948	ENSG00000114948		"""ADAM metallopeptidase domain containing"""	202	protein-coding gene	gene with protein product		603710	"""a disintegrin and metalloproteinase domain 23"""			9693107	Standard	NM_003812		Approved	MDC3	uc002vbq.4	O75077	OTTHUMG00000132919	ENST00000264377.3:c.1229G>A	2.37:g.207425911G>A	ENSP00000264377:p.Arg410His	Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	139	6	0.0431655	NM_003812	A2RU59	Missense_Mutation	SNP	ENST00000264377.3	37	CCDS2369.1	.	.	.	.	.	.	.	.	.	.	G	14.01	2.409037	0.42715	.	.	ENSG00000114948	ENST00000264377;ENST00000374416;ENST00000431817;ENST00000374415	T;T;T	0.09630	2.96;2.96;2.96	5.92	3.8	0.43715	Metallopeptidase, catalytic domain (1);Peptidase M12B, ADAM/reprolysin (2);	0.382911	0.21835	N	0.068402	T	0.06096	0.0158	N	0.17082	0.46	0.29434	N	0.859679	B	0.02656	0.0	B	0.04013	0.001	T	0.14420	-1.0473	10	0.34782	T	0.22	.	6.0539	0.19800	0.1747:0.0:0.6327:0.1926	.	410	O75077	ADA23_HUMAN	H	410;410;304;410	ENSP00000264377:R410H;ENSP00000363537:R410H;ENSP00000363536:R410H	ENSP00000264377:R410H	R	+	2	0	ADAM23	207134156	0.991000	0.36638	1.000000	0.80357	0.997000	0.91878	0.937000	0.28951	1.498000	0.48600	0.655000	0.94253	CGC	.	.	none		0.413	ADAM23-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256431.2	NM_003812	
MOV10L1	54456	hgsc.bcm.edu	37	22	50584201	50584201	+	Silent	SNP	A	A	C	rs2272838	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr22:50584201A>C	ENST00000262794.5	+	19	2672	c.2589A>C	c.(2587-2589)acA>acC	p.T863T	MOV10L1_ENST00000540615.1_Silent_p.T843T|MOV10L1_ENST00000545383.1_Silent_p.T863T|MOV10L1_ENST00000395858.3_Silent_p.T863T|MOV10L1_ENST00000395852.1_5'Flank|MOV10L1_ENST00000395843.1_5'UTR	NM_018995.2	NP_061868.1	Q9BXT6	M10L1_HUMAN	Mov10 RISC complex RNA helicase like 1	863					ATP catabolic process (GO:0006200)|germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	intracellular (GO:0005622)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|magnesium ion binding (GO:0000287)|RNA binding (GO:0003723)	p.T863T(1)		breast(2)|endometrium(2)|kidney(5)|large_intestine(18)|lung(20)|ovary(3)|prostate(1)|skin(9)|stomach(4)|urinary_tract(3)	67		all_cancers(38;3.31e-11)|all_epithelial(38;5.69e-10)|all_lung(38;3.73e-05)|Breast(42;0.000525)|Lung NSC(38;0.000954)|Ovarian(80;0.0367)|Lung SC(80;0.114)		LUAD - Lung adenocarcinoma(64;0.0215)|BRCA - Breast invasive adenocarcinoma(115;0.24)		TCATCACCACATGCAGCAGCT	0.582													a|||	1252	0.25	0.1233	0.3934	5008	,	,		17468	0.252		0.2376	False		,,,				2504	0.3303				p.T863T		Atlas-SNP	.											MOV10L1,NS,carcinoma,0,1	MOV10L1	238	1	1	Substitution - coding silent(1)	stomach(1)	c.A2589C						scavenged	.		,,	676,3730	287.2+/-279.2	56,564,1583	123.0	120.0	121.0		2589,2529,2589	-11.4	0.0	22	dbSNP_100	121	2081,6519	362.5+/-332.8	254,1573,2473	no	coding-synonymous,coding-synonymous,coding-synonymous	MOV10L1	NM_001164104.1,NM_001164105.1,NM_018995.2	,,	310,2137,4056	CC,CA,AA		24.1977,15.3427,21.1979	,,	863/1166,843/1166,863/1212	50584201	2757,10249	2203	4300	6503	SO:0001819	synonymous_variant	54456	exon19			CACCACATGCAGC	AF285604	CCDS14084.1, CCDS54541.1, CCDS54542.1, CCDS54543.1	22q13.33	2014-07-02	2014-07-02		ENSG00000073146	ENSG00000073146			7201	protein-coding gene	gene with protein product	"""cardiac helicase activated by MEF2C protein"""	605794	"""Mov10 (mouse)-like 1"", ""Mov10l1, Moloney leukemia virus 10-like 1, homolog (mouse)"""			11279525	Standard	NM_018995		Approved	DJ402G11.8, DKFZp434B0717, CHAMP	uc003bjj.3	Q9BXT6	OTTHUMG00000044648	ENST00000262794.5:c.2589A>C	22.37:g.50584201A>C		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	64	3	0.046875	NM_018995	A7E211|A8MXC6|B7WPP1|B7Z7R1|F5H403|Q5TGD5|Q8NBD4|Q9NXW3|Q9UFB3|Q9UGX9	Silent	SNP	ENST00000262794.5	37	CCDS14084.1																																																																																			A|0.774;C|0.226	0.226	strong		0.582	MOV10L1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000075009.2	NM_018995	
FAM208B	54906	hgsc.bcm.edu	37	10	5781969	5781969	+	Silent	SNP	A	A	T	rs2797486	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr10:5781969A>T	ENST00000328090.5	+	13	2461	c.1836A>T	c.(1834-1836)acA>acT	p.T612T	RP11-336A10.2_ENST00000411512.2_RNA	NM_017782.4	NP_060252	Q5VWN6	F208B_HUMAN	family with sequence similarity 208, member B	612																	CAGACTTAACAGTTAGCCAAG	0.418													T|||	4192	0.837061	0.8865	0.8804	5008	,	,		21755	0.8135		0.841	False		,,,				2504	0.7597				p.T612T		Atlas-SNP	.											C10orf18,brain,primitive_neuroectodermal_tumour-medulloblastoma,+1,1	.	.	1	0			c.A1836T						PASS	.	T		3286,484		1429,428,28	96.0	88.0	90.0		1836	-7.0	0.0	10	dbSNP_100	90	6864,1384		2851,1162,111	no	coding-synonymous	FAM208B	NM_017782.4		4280,1590,139	TT,TA,AA		16.7798,12.8382,15.5434		612/2431	5781969	10150,1868	1885	4124	6009	SO:0001819	synonymous_variant	54906	exon13			CTTAACAGTTAGC	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.1836A>T	10.37:g.5781969A>T		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	92	4	0.0434783	NM_017782	Q2YD91|Q5VWN5|Q6ZRQ8|Q8IVG4|Q9BUZ7|Q9H5J9|Q9H7A4|Q9H996|Q9NXA1	Silent	SNP	ENST00000328090.5	37	CCDS41485.1																																																																																			A|0.163;T|0.837	0.837	strong		0.418	FAM208B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046571.2	NM_017782	
CCDC132	55610	hgsc.bcm.edu	37	7	92887682	92887682	+	Missense_Mutation	SNP	T	T	C			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr7:92887682T>C	ENST00000305866.5	+	8	682	c.554T>C	c.(553-555)gTa>gCa	p.V185A	CCDC132_ENST00000317751.6_5'UTR|CCDC132_ENST00000251739.5_Missense_Mutation_p.V185A|CCDC132_ENST00000541136.1_5'UTR|CCDC132_ENST00000535481.1_Intron|CCDC132_ENST00000544910.1_Missense_Mutation_p.V155A	NM_017667.3	NP_060137.2	Q96JG6	CC132_HUMAN	coiled-coil domain containing 132	185						extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)				endometrium(1)|large_intestine(2)|lung(5)	8	all_cancers(62;2.64e-11)|all_epithelial(64;1.4e-10)|Breast(17;0.000675)|Lung NSC(181;0.0618)|all_lung(186;0.0837)		STAD - Stomach adenocarcinoma(171;0.000302)			AGAACAGATGTACGGTTAAGT	0.303																																					p.V185A		Atlas-SNP	.											.	CCDC132	136	.	0			c.T554C						PASS	.						117.0	121.0	120.0					7																	92887682		2203	4300	6503	SO:0001583	missense	55610	exon8			CAGATGTACGGTT	AL833112, AK055965, AL832393	CCDS5630.1, CCDS43617.1, CCDS59065.1	7q21.3	2007-07-23			ENSG00000004766	ENSG00000004766			25956	protein-coding gene	gene with protein product						11347906	Standard	NM_024553		Approved	KIAA1861, FLJ20097, DKFZp313I2429	uc003umo.4	Q96JG6	OTTHUMG00000131733	ENST00000305866.5:c.554T>C	7.37:g.92887682T>C	ENSP00000307666:p.Val185Ala	Somatic	255	0	0		WXS	Illumina HiSeq	Phase_I	281	61	0.217082	NM_024553	B3KX22|D1MQ00|F5H5U7|Q75N07|Q8WVK3|Q9H5C6	Missense_Mutation	SNP	ENST00000305866.5	37	CCDS43617.1	.	.	.	.	.	.	.	.	.	.	T	21.2	4.106232	0.77096	.	.	ENSG00000004766	ENST00000251739;ENST00000305866;ENST00000544910;ENST00000458530	.	.	.	5.5	5.5	0.81552	Vacuolar protein sorting-associated protein 54 (1);	0.061028	0.64402	D	0.000004	T	0.60327	0.2260	L	0.46157	1.445	0.80722	D	1	P;P;B	0.51147	0.541;0.942;0.2	B;P;B	0.53549	0.329;0.729;0.049	T	0.55237	-0.8172	9	0.08837	T	0.75	-16.6226	15.9126	0.79482	0.0:0.0:0.0:1.0	.	155;185;185	F5H5U7;Q96JG6;Q96JG6-2	.;CC132_HUMAN;.	A	185;185;155;184	.	ENSP00000251739:V185A	V	+	2	0	CCDC132	92725618	1.000000	0.71417	0.980000	0.43619	0.955000	0.61496	8.040000	0.89188	2.222000	0.72286	0.477000	0.44152	GTA	.	.	none		0.303	CCDC132-019	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341687.1	NM_017667	
CRB2	286204	hgsc.bcm.edu	37	9	126133497	126133497	+	Silent	SNP	C	C	T	rs13290763	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr9:126133497C>T	ENST00000373631.3	+	8	2077	c.2076C>T	c.(2074-2076)tcC>tcT	p.S692S	CRB2_ENST00000373629.2_Silent_p.S360S|CRB2_ENST00000359999.3_Silent_p.S692S	NM_173689.5	NP_775960.4	Q5IJ48	CRUM2_HUMAN	crumbs family member 2	692	Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.				cardiovascular system development (GO:0072358)|maintenance of epithelial cell apical/basal polarity (GO:0045199)|mesoderm formation (GO:0001707)|negative regulation of endopeptidase activity (GO:0010951)|notochord formation (GO:0014028)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|somitogenesis (GO:0001756)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	calcium ion binding (GO:0005509)|enzyme binding (GO:0019899)			NS(2)|breast(1)|cervix(1)|endometrium(2)|lung(11)|ovary(1)|prostate(2)|skin(3)	23						CCAATGACTCCGCAGCTGGCC	0.617													C|||	981	0.195887	0.053	0.1729	5008	,	,		20100	0.254		0.2734	False		,,,				2504	0.2658				p.S692S		Atlas-SNP	.											.	CRB2	86	.	0			c.C2076T						PASS	.	C		373,4033		16,341,1846	129.0	138.0	135.0		2076	-9.1	0.0	9	dbSNP_121	135	2696,5904		427,1842,2031	no	coding-synonymous	CRB2	NM_173689.5		443,2183,3877	TT,TC,CC		31.3488,8.4657,23.5968		692/1286	126133497	3069,9937	2203	4300	6503	SO:0001819	synonymous_variant	286204	exon8			TGACTCCGCAGCT	AK095783	CCDS6852.2	9q33.2	2014-02-06	2014-02-06		ENSG00000148204	ENSG00000148204			18688	protein-coding gene	gene with protein product		609720	"""crumbs homolog 2 (Drosophila)"""			14767562	Standard	XM_005251934		Approved	FLJ38464, FLJ16786	uc004bnx.1	Q5IJ48	OTTHUMG00000020638	ENST00000373631.3:c.2076C>T	9.37:g.126133497C>T		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	91	4	0.043956	NM_173689	A2A3N4|Q0QD46|Q5JS41|Q5JS43|Q6ZTA9|Q6ZWI6	Silent	SNP	ENST00000373631.3	37	CCDS6852.2																																																																																			C|0.763;T|0.237	0.237	strong		0.617	CRB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053990.3	NM_173689	
ASAH1	427	hgsc.bcm.edu	37	8	17942220	17942220	+	5'Flank	SNP	T	T	C	rs3213606	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr8:17942220T>C	ENST00000262097.6	-	0	0				CTD-2547L16.1_ENST00000505114.2_RNA|CTD-2547L16.1_ENST00000517747.1_RNA|ASAH1_ENST00000381733.4_Missense_Mutation_p.I31V|ASAH1_ENST00000314146.10_Missense_Mutation_p.I31V|ASAH1_ENST00000520051.1_5'UTR|CTD-2547L16.1_ENST00000517798.1_RNA|CTD-2547L16.1_ENST00000521775.1_RNA|ASAH1_ENST00000417108.2_5'Flank|CTD-2547L16.1_ENST00000499554.2_RNA|ASAH1_ENST00000520781.1_5'Flank	NM_177924.3	NP_808592.2	Q13510	ASAH1_HUMAN	N-acylsphingosine amidohydrolase (acid ceramidase) 1						cell death (GO:0008219)|ceramide metabolic process (GO:0006672)|glycosphingolipid metabolic process (GO:0006687)|lung development (GO:0030324)|response to organic substance (GO:0010033)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)	catalytic activity (GO:0003824)|ceramidase activity (GO:0017040)	p.I31V(1)		breast(1)|endometrium(2)|large_intestine(4)|lung(2)	9				Colorectal(111;0.0646)|COAD - Colon adenocarcinoma(73;0.228)		AATCCCAGAATTGAGGCCTCG	0.577											OREG0018581	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	T|||	22	0.00439297	0.0	0.0	5008	,	,		16739	0.0218		0.0	False		,,,				2504	0.0				p.I31V		Atlas-SNP	.											ASAH1_ENST00000381733,NS,carcinoma,0,1	ASAH1	71	1	1	Substitution - Missense(1)	stomach(1)	c.A91G						PASS	.	T	VAL/ILE,VAL/ILE	1,4405		0,1,2202	49.0	50.0	50.0		91,91	-3.6	0.0	8	dbSNP_106	50	4,8596		0,4,4296	yes	missense,missense	ASAH1	NM_001127505.1,NM_004315.4	29,29	0,5,6498	CC,CT,TT		0.0465,0.0227,0.0384	,	31/390,31/412	17942220	5,13001	2203	4300	6503	SO:0001631	upstream_gene_variant	427	exon1			CCAGAATTGAGGC	U70063	CCDS6005.1, CCDS6006.1, CCDS47813.1	8p22	2007-03-27	2002-09-11	2002-09-13	ENSG00000104763	ENSG00000104763			735	protein-coding gene	gene with protein product		613468	"""N-acylsphingosine amidohydrolase (acid ceramidase)"""	ASAH		8955159, 10610716	Standard	NM_004315		Approved	AC, PHP32, FLJ21558	uc003wyn.2	Q13510	OTTHUMG00000096997		8.37:g.17942220T>C	Exception_encountered	Somatic	79	0	0	721	WXS	Illumina HiSeq	Phase_I	83	4	0.0481928	NM_001127505	E9PDS0|Q6W898|Q96AS2	Missense_Mutation	SNP	ENST00000262097.6	37	CCDS6006.1	16	0.007326007326007326	0	0.0	0	0.0	16	0.027972027972027972	0	0.0	.	7.180	0.589465	0.13812	2.27E-4	4.65E-4	ENSG00000104763	ENST00000381733;ENST00000314146	T;T	0.70282	-0.35;-0.47	3.05	-3.58	0.04597	.	7739.210000	0.00166	N	0.000001	T	0.22704	0.0548	N	0.08118	0	0.09310	N	0.999993	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.34700	-0.9818	10	0.09590	T	0.72	-1.6773	8.0324	0.30472	0.0:0.5287:0.0:0.4713	rs3213606;rs17636247;rs52812973;rs3213606	31;31	E9PDS0;Q13510-2	.;.	V	31	ENSP00000371152:I31V;ENSP00000326970:I31V	ENSP00000326970:I31V	I	-	1	0	ASAH1	17986500	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.724000	0.04947	-0.659000	0.05359	-0.313000	0.08912	ATT	T|0.991;C|0.009	0.009	strong		0.577	ASAH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214077.2	NM_004315	
MSX1	4487	hgsc.bcm.edu	37	4	4861745	4861745	+	Missense_Mutation	SNP	C	C	G	rs36059701	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr4:4861745C>G	ENST00000382723.4	+	1	353	c.119C>G	c.(118-120)gCa>gGa	p.A40G		NM_002448.3	NP_002439.2	P28360	MSX1_HUMAN	msh homeobox 1	40	Poly-Ala.				activation of meiosis (GO:0090427)|anterior/posterior pattern specification (GO:0009952)|BMP signaling pathway involved in heart development (GO:0061312)|bone morphogenesis (GO:0060349)|cartilage morphogenesis (GO:0060536)|cell morphogenesis (GO:0000902)|cellular response to nicotine (GO:0071316)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic nail plate morphogenesis (GO:0035880)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|face morphogenesis (GO:0060325)|in utero embryonic development (GO:0001701)|mammary gland epithelium development (GO:0061180)|mesenchymal cell proliferation (GO:0010463)|midbrain development (GO:0030901)|middle ear morphogenesis (GO:0042474)|muscle organ development (GO:0007517)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of striated muscle cell differentiation (GO:0051154)|negative regulation of transcription regulatory region DNA binding (GO:2000678)|odontogenesis of dentin-containing tooth (GO:0042475)|palate development (GO:0060021)|pituitary gland development (GO:0021983)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator (GO:1902255)|positive regulation of mesenchymal cell apoptotic process (GO:2001055)|protein localization to nucleus (GO:0034504)|protein stabilization (GO:0050821)|regulation of odontogenesis (GO:0042481)|signal transduction involved in regulation of gene expression (GO:0023019)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	p53 binding (GO:0002039)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity (GO:0000982)|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 negative regulation of transcription (GO:0001227)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)			endometrium(3)|lung(5)|ovary(1)|prostate(1)|urinary_tract(1)	11				UCEC - Uterine corpus endometrioid carcinoma (64;0.163)		gcggccACGGCAGCCGCCATG	0.716													C|||	519	0.103634	0.0893	0.1037	5008	,	,		6085	0.0565		0.165	False		,,,				2504	0.1084				p.A40G		Atlas-SNP	.											MSX1,NS,carcinoma,0,1	MSX1	19	1	0			c.C119G	GRCh37	CM045070	MSX1	M	rs36059701	scavenged	.	C	GLY/ALA	241,2261		15,211,1025	3.0	4.0	4.0		119	2.9	0.4	4	dbSNP_126	4	677,4129		58,561,1784	no	missense	MSX1	NM_002448.3	60	73,772,2809	GG,GC,CC		14.0866,9.6323,12.5616	benign	40/304	4861745	918,6390	1251	2403	3654	SO:0001583	missense	4487	exon1			CCACGGCAGCCGC	M97676	CCDS3378.2	4p16.2	2011-06-20	2006-11-21		ENSG00000163132	ENSG00000163132		"""Homeoboxes / ANTP class : NKL subclass"""	7391	protein-coding gene	gene with protein product		142983	"""msh (Drosophila) homeo box homolog 1 (formerly homeo box 7)"", ""msh homeobox homolog 1 (Drosophila)"""	HOX7		1685479, 1973146	Standard	NM_002448		Approved	HYD1, OFC5	uc003gif.3	P28360	OTTHUMG00000090335	ENST00000382723.4:c.119C>G	4.37:g.4861745C>G	ENSP00000372170:p.Ala40Gly	Somatic	5	1	0.2		WXS	Illumina HiSeq	Phase_I	10	8	0.8	NM_002448	A0SZU5|A8K3M1|Q96NY4	Missense_Mutation	SNP	ENST00000382723.4	37	CCDS3378.2	290	0.13278388278388278	53	0.10772357723577236	45	0.12430939226519337	44	0.07692307692307693	148	0.19525065963060687	C	6.955	0.546124	0.13312	0.096323	0.140866	ENSG00000163132	ENST00000382723	D	0.95885	-3.84	4.66	2.92	0.33932	.	0.650131	0.15386	N	0.265060	T	0.00552	0.0018	N	0.24115	0.695	0.51767	P	6.20000000000065E-5	B	0.16166	0.016	B	0.15870	0.014	T	0.44003	-0.9356	9	0.11182	T	0.66	-4.3518	5.025	0.14379	0.1663:0.6515:0.0:0.1822	rs36059701	34	P28360	MSX1_HUMAN	G	40	ENSP00000372170:A40G	ENSP00000372170:A40G	A	+	2	0	MSX1	4912646	0.996000	0.38824	0.367000	0.25926	0.047000	0.14425	0.572000	0.23684	0.390000	0.25115	0.491000	0.48974	GCA	C|0.868;G|0.132	0.132	strong		0.716	MSX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206700.3		
DNAJC6	9829	hgsc.bcm.edu	37	1	65860687	65860687	+	Silent	SNP	A	A	C	rs4582839	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr1:65860687A>C	ENST00000395325.3	+	13	1996	c.1839A>C	c.(1837-1839)ccA>ccC	p.P613P	DNAJC6_ENST00000371069.4_Silent_p.P670P|DNAJC6_ENST00000263441.7_Silent_p.P600P	NM_014787.3	NP_055602.1	O75061	AUXI_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 6	613	Pro-rich.				cell death (GO:0008219)|clathrin coat disassembly (GO:0072318)|membrane organization (GO:0061024)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of clathrin-mediated endocytosis (GO:2000369)	cytosol (GO:0005829)|synapse (GO:0045202)	protein tyrosine phosphatase activity (GO:0004725)			NS(1)|breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(22)|ovary(1)|prostate(2)|skin(1)	39						TTCTCCAGCCAACAAGAAGTC	0.423													C|||	3795	0.757788	0.9811	0.6282	5008	,	,		19335	0.7927		0.5924	False		,,,				2504	0.682				p.P670P		Atlas-SNP	.											.	DNAJC6	104	.	0			c.A2010C						PASS	.	C		4022,384	189.9+/-215.9	1846,330,27	151.0	157.0	155.0		1839	-4.8	0.8	1	dbSNP_111	155	5023,3577	517.8+/-379.1	1449,2125,726	no	coding-synonymous	DNAJC6	NM_014787.2		3295,2455,753	CC,CA,AA		41.593,8.7154,30.4552		613/914	65860687	9045,3961	2203	4300	6503	SO:0001819	synonymous_variant	9829	exon13			CCAGCCAACAAGA	AB007942	CCDS30739.1, CCDS58004.1, CCDS58005.1	1p31.3	2011-09-02			ENSG00000116675	ENSG00000116675		"""Heat shock proteins / DNAJ (HSP40)"""	15469	protein-coding gene	gene with protein product	"""auxilin"""	608375				9455484, 11147971	Standard	NM_001256864		Approved	KIAA0473	uc001dce.2	O75061	OTTHUMG00000009066	ENST00000395325.3:c.1839A>C	1.37:g.65860687A>C		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	119	6	0.0504202	NM_001256864	B7Z3V8|D3DQ65|D3DQ66|Q32M66|Q4G0K1|Q5T614|Q5T615	Silent	SNP	ENST00000395325.3	37	CCDS30739.1																																																																																			A|0.300;C|0.700	0.700	strong		0.423	DNAJC6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000025134.1		
F8	2157	hgsc.bcm.edu	37	X	154158201	154158201	+	Silent	SNP	T	T	G	rs1800292	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chrX:154158201T>G	ENST00000360256.4	-	14	4064	c.3864A>C	c.(3862-3864)tcA>tcC	p.S1288S		NM_000132.3	NP_000123.1	P00451	FA8_HUMAN	coagulation factor VIII, procoagulant component	1288	B.				acute-phase response (GO:0006953)|blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell adhesion (GO:0007155)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	copper ion binding (GO:0005507)|oxidoreductase activity (GO:0016491)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(27)|liver(1)|lung(47)|ovary(5)|pancreas(3)|prostate(1)|skin(5)|upper_aerodigestive_tract(5)|urinary_tract(2)	120	all_cancers(53;7.19e-17)|all_epithelial(53;9.83e-11)|all_lung(58;6.63e-07)|Lung NSC(58;2.08e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)				Coagulation Factor IX(DB00100)|Drotrecogin alfa(DB00055)	CCCCTTTTTTTGAGAAATGAG	0.378													T|||	606	0.16053	0.0499	0.1484	3775	,	,		13873	0.1359		0.0527	False		,,,				2504	0.2526				p.S1288S		Atlas-SNP	.											.	F8	646	.	0			c.A3864C	GRCh37	CI992004	F8	I	rs1800292	PASS	.	T		238,3597		7,188,36,1437,535	164.0	141.0	149.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	3864	2.5	0.1	X	dbSNP_89	149	608,6119		22,381,183,2025,1688	no	coding-synonymous	F8	NM_000132.3		29,569,219,3462,2223	GG,GT,G,TT,T		9.0382,6.206,8.0098		1288/2352	154158201	846,9716	2203	4299	6502	SO:0001819	synonymous_variant	2157	exon14			TTTTTTTGAGAAA	M90707	CCDS35457.1, CCDS44026.1	Xq28	2014-09-17	2008-07-29		ENSG00000185010	ENSG00000185010			3546	protein-coding gene	gene with protein product	"""Factor VIIIF8B"", ""hemophilia A"""	300841		F8C		6438528, 3935400	Standard	NM_000132		Approved	FVIII, DXS1253E, HEMA	uc004fmt.3	P00451	OTTHUMG00000022688	ENST00000360256.4:c.3864A>C	X.37:g.154158201T>G		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	119	5	0.0420168	NM_000132	Q14286|Q5HY69	Silent	SNP	ENST00000360256.4	37	CCDS35457.1																																																																																			T|0.888;0|0.022	.	strong		0.378	F8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058869.4		
FUT10	84750	hgsc.bcm.edu	37	8	33246538	33246538	+	Silent	SNP	A	A	G	rs16880849	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr8:33246538A>G	ENST00000327671.5	-	4	1786	c.1155T>C	c.(1153-1155)gaT>gaC	p.D385D	FUT10_ENST00000518076.1_5'UTR|FUT10_ENST00000518672.1_Silent_p.D357D|FUT10_ENST00000524021.1_Silent_p.D357D|FUT10_ENST00000335589.3_Silent_p.D323D	NM_032664.3	NP_116053.3	Q6P4F1	FUT10_HUMAN	fucosyltransferase 10 (alpha (1,3) fucosyltransferase)	385					embryo development (GO:0009790)|fertilization (GO:0009566)|fucosylation (GO:0036065)|hemopoiesis (GO:0030097)|L-fucose catabolic process (GO:0042355)|nervous system development (GO:0007399)|protein folding (GO:0006457)|protein glycosylation (GO:0006486)|protein targeting (GO:0006605)|wound healing (GO:0042060)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	alpha-(1->3)-fucosyltransferase activity (GO:0046920)	p.D385D(1)		cervix(1)|endometrium(1)|large_intestine(7)|liver(1)|lung(9)|ovary(1)|pancreas(1)|prostate(3)|stomach(3)|upper_aerodigestive_tract(2)	29				KIRC - Kidney renal clear cell carcinoma(67;0.129)|Kidney(114;0.154)		ACTCAAATGCATCGATGTAAT	0.498													A|||	1496	0.298722	0.1808	0.17	5008	,	,		22022	0.4692		0.1938	False		,,,				2504	0.4816				p.D385D		Atlas-SNP	.											FUT10,NS,carcinoma,0,1	FUT10	62	1	1	Substitution - coding silent(1)	stomach(1)	c.T1155C						scavenged	.	A		916,3490	349.5+/-310.4	76,764,1363	246.0	207.0	220.0		1155	-0.1	0.9	8	dbSNP_123	220	1748,6852	317.0+/-313.0	177,1394,2729	no	coding-synonymous	FUT10	NM_032664.3		253,2158,4092	GG,GA,AA		20.3256,20.7898,20.4829		385/480	33246538	2664,10342	2203	4300	6503	SO:0001819	synonymous_variant	84750	exon4			AAATGCATCGATG	AJ512465	CCDS6088.1	8p12	2013-02-26			ENSG00000172728	ENSG00000172728		"""Fucosyltransferases"""	19234	protein-coding gene	gene with protein product							Standard	NM_032664		Approved		uc003xje.3	Q6P4F1	OTTHUMG00000163954	ENST00000327671.5:c.1155T>C	8.37:g.33246538A>G		Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	139	2	0.0143885	NM_032664	A8KAC8|Q70GG3|Q8IVI6|Q8IVI7|Q8IVJ3|Q8TE43|Q9BSR3	Silent	SNP	ENST00000327671.5	37	CCDS6088.1																																																																																			A|0.769;G|0.231	0.231	strong		0.498	FUT10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376540.1	NM_032664	
NCOR1	9611	hgsc.bcm.edu	37	17	15960883	15960883	+	Missense_Mutation	SNP	G	G	T			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr17:15960883G>T	ENST00000268712.3	-	40	6594	c.6337C>A	c.(6337-6339)Caa>Aaa	p.Q2113K	NCOR1_ENST00000395857.3_Missense_Mutation_p.Q697K|NCOR1_ENST00000395851.1_Missense_Mutation_p.Q2010K	NM_006311.3	NP_006302.2	O75376	NCOR1_HUMAN	nuclear receptor corepressor 1	2113	ID1. {ECO:0000250}.|Interaction with C1D. {ECO:0000250}.				CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation (GO:0002361)|cellular lipid metabolic process (GO:0044255)|cholesterol homeostasis (GO:0042632)|chromatin modification (GO:0016568)|circadian regulation of gene expression (GO:0032922)|definitive erythrocyte differentiation (GO:0060318)|gene expression (GO:0010467)|negative regulation of JNK cascade (GO:0046329)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of histone deacetylation (GO:0031065)|regulation of fatty acid transport (GO:2000191)|regulation of glycolytic process by negative regulation of transcription from RNA polymerase II promoter (GO:0072362)|regulation of lipid transport by negative regulation of transcription from RNA polymerase II promoter (GO:0072368)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|spindle assembly (GO:0051225)|thalamus development (GO:0021794)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)|transcription factor complex (GO:0005667)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|histone deacetylase binding (GO:0042826)|histone deacetylase regulator activity (GO:0035033)|nuclear hormone receptor binding (GO:0035257)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)	p.Q2113E(1)		NS(2)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(17)|lung(26)|ovary(1)|prostate(7)|skin(2)|upper_aerodigestive_tract(6)|urinary_tract(10)	107				UCEC - Uterine corpus endometrioid carcinoma (92;0.101)		CCTGGTCTTTGATGATGGACA	0.418																																					p.Q2113K		Atlas-SNP	.											NCOR1,NS,carcinoma,0,1	NCOR1	240	1	1	Substitution - Missense(1)	breast(1)	c.C6337A						scavenged	.						120.0	122.0	121.0					17																	15960883		2203	4300	6503	SO:0001583	missense	9611	exon40			GTCTTTGATGATG	AF044209	CCDS11175.1, CCDS54094.1, CCDS54095.1	17p11.2	2014-06-12	2010-06-10		ENSG00000141027	ENSG00000141027			7672	protein-coding gene	gene with protein product	"""thyroid hormone- and retinoic acid receptor-associated corepressor 1"", ""protein phosphatase 1, regulatory subunit 109"""	600849	"""nuclear receptor co-repressor 1"""			7566114, 9724795	Standard	NM_006311		Approved	N-CoR, hCIT529I10, TRAC1, hN-CoR, KIAA1047, MGC104216, PPP1R109	uc002gpo.3	O75376	OTTHUMG00000059309	ENST00000268712.3:c.6337C>A	17.37:g.15960883G>T	ENSP00000268712:p.Gln2113Lys	Somatic	193	0	0		WXS	Illumina HiSeq	Phase_I	158	4	0.0253165	NM_006311	B3DLF8|E9PGV6|Q86YY0|Q9UPV5|Q9UQ18	Missense_Mutation	SNP	ENST00000268712.3	37	CCDS11175.1	.	.	.	.	.	.	.	.	.	.	G	17.00	3.275602	0.59649	.	.	ENSG00000141027	ENST00000268712;ENST00000395851;ENST00000395849;ENST00000395857	T;T;T	0.44482	0.92;1.49;0.93	6.0	6.0	0.97389	.	0.165937	0.56097	D	0.000031	T	0.31638	0.0803	N	0.08118	0	0.58432	D	0.999998	B;B;B;P;P;B	0.49253	0.082;0.203;0.084;0.921;0.561;0.338	B;B;B;P;B;B	0.49708	0.062;0.064;0.031;0.62;0.267;0.235	T	0.07065	-1.0792	10	0.02654	T	1	-0.8053	19.4831	0.95018	0.0:0.0:1.0:0.0	.	923;2017;2113;2010;633;127	B4DZ48;E7EVK1;O75376;O75376-2;Q86YY1;Q86YY2	.;.;NCOR1_HUMAN;.;.;.	K	2113;2010;2017;697	ENSP00000268712:Q2113K;ENSP00000379192:Q2010K;ENSP00000379198:Q697K	ENSP00000268712:Q2113K	Q	-	1	0	NCOR1	15901608	1.000000	0.71417	0.998000	0.56505	0.996000	0.88848	9.147000	0.94646	2.848000	0.98002	0.655000	0.94253	CAA	.	.	none		0.418	NCOR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131751.5	NM_006311	
PZP	5858	hgsc.bcm.edu	37	12	9312951	9312951	+	Missense_Mutation	SNP	G	G	A	rs57006764	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr12:9312951G>A	ENST00000261336.2	-	24	3036	c.3008C>T	c.(3007-3009)aCg>aTg	p.T1003M	PZP_ENST00000381997.2_Missense_Mutation_p.T789M|PZP_ENST00000539983.1_5'Flank	NM_002864.2	NP_002855.2	P20742	PZP_HUMAN	pregnancy-zone protein	1003			T -> M (in dbSNP:rs57006764).		female pregnancy (GO:0007565)|negative regulation of endopeptidase activity (GO:0010951)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(21)|lung(46)|ovary(3)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(5)	102						GATCTCCTGCGTCAGCTGCTG	0.428													G|||	1356	0.270767	0.1619	0.2695	5008	,	,		-128	0.4762		0.1909	False		,,,				2504	0.2894				p.T1003M	Melanoma(125;1402 1695 4685 34487 38571)	Atlas-SNP	.											PZP_ENST00000381997,NS,carcinoma,+1,2	PZP	422	2	0			c.C3008T						PASS	.	G	MET/THR	710,3696	293.6+/-282.7	68,574,1561	130.0	119.0	123.0		3008	3.7	0.0	12	dbSNP_129	123	1456,7144	278.2+/-293.3	116,1224,2960	yes	missense	PZP	NM_002864.2	81	184,1798,4521	AA,AG,GG		16.9302,16.1144,16.6539	probably-damaging	1003/1483	9312951	2166,10840	2203	4300	6503	SO:0001583	missense	5858	exon24			TCCTGCGTCAGCT	X54380, M24416, X51541	CCDS8600.1	12p13-p12.2	2008-02-01			ENSG00000126838	ENSG00000126838			9750	protein-coding gene	gene with protein product		176420					Standard	NM_002864		Approved	CPAMD6	uc001qvl.3	P20742	OTTHUMG00000154915	ENST00000261336.2:c.3008C>T	12.37:g.9312951G>A	ENSP00000261336:p.Thr1003Met	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	116	7	0.0603448	NM_002864	A6ND27|Q15273|Q2NKL2|Q7M4N7	Missense_Mutation	SNP	ENST00000261336.2	37	CCDS8600.1	577	0.2641941391941392	105	0.21341463414634146	92	0.2541436464088398	253	0.4423076923076923	127	0.16754617414248021	G	11.01	1.514300	0.27123	0.161144	0.169302	ENSG00000126838	ENST00000261336;ENST00000381997	T;T	0.40225	1.04;1.04	4.56	3.67	0.42095	Terpenoid cylases/protein prenyltransferase alpha-alpha toroid (1);	0.075423	0.48286	U	0.000182	T	0.00012	0.0000	M	0.90369	3.11	0.43203	P	0.004940999999999973	D;D	0.89917	1.0;1.0	D;D	0.83275	0.951;0.996	T	0.38090	-0.9677	9	0.87932	D	0	.	8.6441	0.33994	0.0835:0.1509:0.7656:0.0	rs57006764;rs61740800	789;1003	P20742-2;P20742	.;PZP_HUMAN	M	1003;789	ENSP00000261336:T1003M;ENSP00000371427:T789M	ENSP00000261336:T1003M	T	-	2	0	PZP	9204218	0.993000	0.37304	0.031000	0.17742	0.009000	0.06853	2.458000	0.45014	1.044000	0.40200	0.563000	0.77884	ACG	G|0.805;A|0.195	0.195	strong		0.428	PZP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337624.1	NM_002864	
SPATA31A6	389730	hgsc.bcm.edu	37	9	43628679	43628679	+	Missense_Mutation	SNP	G	G	A	rs2491538	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr9:43628679G>A	ENST00000332857.6	-	3	291	c.263C>T	c.(262-264)cCg>cTg	p.P88L	SPATA31A6_ENST00000496386.1_5'UTR	NM_001145196.1	NP_001138668.1	Q5VVP1	S31A6_HUMAN	SPATA31 subfamily A, member 6	88					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											CAGGCCTCTCGGGCACTCTCT	0.582													g|||	56	0.0111821	0.0	0.0014	5008	,	,		9767	0.0228		0.001	False		,,,				2504	0.0317				p.P88L		Atlas-SNP	.											FAM75A6,right_upper_lobe,carcinoma,0,2	.	.	2	0			c.C263T						scavenged	.																																			SO:0001583	missense	389730	exon3			CCTCTCGGGCACT		CCDS75837.1	9p11.2	2012-10-15	2012-10-12	2012-10-12	ENSG00000185775	ENSG00000185775			32006	protein-coding gene	gene with protein product			"""family with sequence similarity 75, member A6"""	FAM75A6		20850414	Standard	NM_001145196		Approved	OTTHUMG00000013224	uc011lrb.2	Q5VVP1	OTTHUMG00000013224	ENST00000332857.6:c.263C>T	9.37:g.43628679G>A	ENSP00000329825:p.Pro88Leu	Somatic	556	0	0		WXS	Illumina HiSeq	Phase_I	462	5	0.0108225	NM_001145196		Missense_Mutation	SNP	ENST00000332857.6	37	CCDS47973.1	.	.	.	.	.	.	.	.	.	.	C	0.005	-2.182813	0.00308	.	.	ENSG00000185775	ENST00000332857	T	0.03272	3.99	2.08	-2.63	0.06133	.	0.630203	0.12182	N	0.492007	T	0.01029	0.0034	N	0.01438	-0.865	0.09310	N	1	B	0.09022	0.002	B	0.01281	0.0	T	0.45411	-0.9263	10	0.19147	T	0.46	.	0.1644	0.00107	0.3583:0.2399:0.1662:0.2356	.	88	Q5VVP1	F75A6_HUMAN	L	88	ENSP00000329825:P88L	ENSP00000329825:P88L	P	-	2	0	FAM75A6	43568675	0.003000	0.15002	0.015000	0.15790	0.012000	0.07955	-0.050000	0.11904	-0.592000	0.05851	-0.751000	0.03497	CCG	G|0.996;A|0.004	0.004	strong		0.582	SPATA31A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036987.1	NM_001145196	
FUT6	2528	hgsc.bcm.edu	37	19	5832209	5832209	+	Missense_Mutation	SNP	G	G	A	rs778805	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr19:5832209G>A	ENST00000318336.4	-	3	1564	c.370C>T	c.(370-372)Ccg>Tcg	p.P124S	FUT6_ENST00000527106.1_Missense_Mutation_p.P124S|FUT6_ENST00000592563.1_Missense_Mutation_p.P124S|FUT6_ENST00000524754.1_Missense_Mutation_p.P124S|FUT6_ENST00000286955.5_Missense_Mutation_p.P124S	NM_000150.2	NP_000141.1	P51993	FUT6_HUMAN	fucosyltransferase 6 (alpha (1,3) fucosyltransferase)	124			P -> S (found in alpha(1,3)- fucosyltransferase-deficient individuals; results in partial enzyme inactivation; complete enzyme inactivation when associated with V-244 and G-303; dbSNP:rs778805). {ECO:0000269|PubMed:11102976, ECO:0000269|Ref.4}.		fucosylation (GO:0036065)|L-fucose catabolic process (GO:0042355)|protein glycosylation (GO:0006486)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	3-galactosyl-N-acetylglucosaminide 4-alpha-L-fucosyltransferase activity (GO:0017060)|alpha-(1->3)-fucosyltransferase activity (GO:0046920)|fucosyltransferase activity (GO:0008417)			endometrium(2)|kidney(1)|large_intestine(1)|lung(2)	6						TGCCGCCTCGGGGAGCGTGGG	0.607													G|||	2480	0.495208	0.643	0.4928	5008	,	,		16047	0.6121		0.3131	False		,,,				2504	0.364				p.P124S		Atlas-SNP	.											FUT6,NS,carcinoma,+1,1	FUT6	30	1	0			c.C370T	GRCh37	CM940794	FUT6	M	rs778805	scavenged	.	G	SER/PRO,SER/PRO	2612,1794	638.8+/-397.0	766,1080,357	71.0	60.0	64.0		370,370	2.1	0.0	19	dbSNP_86	64	2849,5751	447.3+/-361.5	453,1943,1904	yes	missense,missense	FUT6	NM_000150.2,NM_001040701.1	74,74	1219,3023,2261	AA,AG,GG		33.1279,40.7172,41.9883	possibly-damaging,possibly-damaging	124/360,124/360	5832209	5461,7545	2203	4300	6503	SO:0001583	missense	2528	exon3			GCCTCGGGGAGCG		CCDS12152.1	19p13.3	2013-02-26			ENSG00000156413	ENSG00000156413	2.4.1.65	"""Fucosyltransferases"""	4017	protein-coding gene	gene with protein product	"""alpha-(1,3)-fucosyltransferase"", ""galactoside 3-L-fucosyltransferase"""	136836				1520296, 7782074	Standard	NM_001040701		Approved	FT1A, FCT3A, FucT-VI, FLJ40754	uc002mdh.1	P51993	OTTHUMG00000167335	ENST00000318336.4:c.370C>T	19.37:g.5832209G>A	ENSP00000313398:p.Pro124Ser	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	106	4	0.0377358	NM_000150	A6NEX0|D6W637|Q9UND8	Missense_Mutation	SNP	ENST00000318336.4	37	CCDS12152.1	1053	0.48214285714285715	319	0.6483739837398373	168	0.46408839779005523	329	0.5751748251748252	237	0.31266490765171506	G	10.20	1.286073	0.23478	0.592828	0.331279	ENSG00000156413	ENST00000524754;ENST00000527106;ENST00000318336;ENST00000286955;ENST00000341530;ENST00000529165	T;T;T;T;T	0.24350	1.86;1.86;1.86;1.86;1.86	3.17	2.11	0.27256	.	0.206719	0.32970	N	0.005421	T	0.00012	0.0000	M	0.63428	1.95	0.80722	P	0.0	B;B	0.19331	0.035;0.006	B;B	0.29440	0.102;0.063	T	0.32295	-0.9912	9	0.41790	T	0.15	.	12.3946	0.55378	0.0:0.0:0.8278:0.1722	rs778805;rs4041472;rs17205925;rs17855738;rs58152597;rs778805	124;124	C9J8A2;P51993	.;FUT6_HUMAN	S	124	ENSP00000431708:P124S;ENSP00000432954:P124S;ENSP00000313398:P124S;ENSP00000286955:P124S;ENSP00000436547:P124S	ENSP00000286955:P124S	P	-	1	0	FUT6	5783209	0.573000	0.26676	0.000000	0.03702	0.000000	0.00434	1.907000	0.39897	0.145000	0.18977	-2.014000	0.00435	CCG	G|0.555;A|0.445	0.445	strong		0.607	FUT6-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394218.2	NM_000150	
MUC20	200958	hgsc.bcm.edu	37	3	195452951	195452951	+	Missense_Mutation	SNP	G	G	C	rs2688542		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr3:195452951G>C	ENST00000447234.2	+	2	1603	c.1477G>C	c.(1477-1479)Gat>Cat	p.D493H	MUC20_ENST00000436408.1_Missense_Mutation_p.D493H|MUC20_ENST00000445522.2_Missense_Mutation_p.D458H|MUC20_ENST00000320736.6_Missense_Mutation_p.D322H	NM_001282506.1	NP_001269435.1	Q8N307	MUC20_HUMAN	mucin 20, cell surface associated	493	Involved in oligomerization.		Missing. {ECO:0000269|PubMed:14702039}.	D -> H (in Ref. 1; BAD06718/BAD06720, 2; AAQ88814, 3; BAC11428 and 5; AAH44243). {ECO:0000305}.	activation of MAPK activity (GO:0000187)|cellular protein metabolic process (GO:0044267)|hepatocyte growth factor receptor signaling pathway (GO:0048012)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein homooligomerization (GO:0051260)	basal plasma membrane (GO:0009925)|cell projection (GO:0042995)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)				NS(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(4)|skin(4)|stomach(3)|upper_aerodigestive_tract(1)	23	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)	Lung NSC(153;0.191)	Epithelial(36;1e-21)|all cancers(36;9.02e-20)|OV - Ovarian serous cystadenocarcinoma(49;1.6e-18)|Lung(62;0.000104)|LUSC - Lung squamous cell carcinoma(58;0.000128)	GBM - Glioblastoma multiforme(46;1.66e-05)		AGCTGCACCTGATGCCACGGT	0.602																																					p.D322H		Atlas-SNP	.											MUC20,NS,carcinoma,0,1	MUC20	84	1	0			c.G964C						scavenged	.						53.0	48.0	49.0					3																	195452951		2178	4281	6459	SO:0001583	missense	200958	exon3			GCACCTGATGCCA	AB037780	CCDS63877.1	3q29	2008-08-07	2006-03-14		ENSG00000176945	ENSG00000176945		"""Mucins"""	23282	protein-coding gene	gene with protein product		610360				14565953	Standard	NM_001282506		Approved	FLJ14408, KIAA1359	uc010hzo.3	Q8N307	OTTHUMG00000155823	ENST00000447234.2:c.1477G>C	3.37:g.195452951G>C	ENSP00000414350:p.Asp493His	Somatic	313	1	0.00319489		WXS	Illumina HiSeq	Phase_I	321	12	0.0373832	NM_152673	Q6UX97|Q76I83|Q76I85|Q86ST8|Q8NBY6|Q96KA1|Q9P2I8	Missense_Mutation	SNP	ENST00000447234.2	37		1354	0.61996336996337	233	0.4735772357723577	204	0.56353591160221	451	0.7884615384615384	466	0.6147757255936676	G	8.698	0.909135	0.17833	.	.	ENSG00000176945	ENST00000447234;ENST00000320736;ENST00000436408;ENST00000445522	T;T;T;T	0.20463	2.51;2.58;2.67;2.07	3.94	2.12	0.27331	.	1.625610	0.03967	N	0.290924	T	0.00012	0.0000	L	0.29908	0.895	0.80722	P	0.0	D	0.54964	0.969	P	0.50490	0.642	T	0.41179	-0.9523	9	0.36615	T	0.2	1.5642	5.8281	0.18564	0.2458:0.0:0.7542:0.0	rs2688542;rs3828412	322	E9PH32	.	H	493;322;493;458	ENSP00000414350:D493H;ENSP00000325431:D322H;ENSP00000396774:D493H;ENSP00000405629:D458H	ENSP00000325431:D322H	D	+	1	0	MUC20	196938622	0.001000	0.12720	0.002000	0.10522	0.052000	0.14988	0.431000	0.21444	0.428000	0.26173	0.514000	0.50259	GAT	G|0.379;C|0.621	0.621	strong		0.602	MUC20-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000341835.1	NM_152673	
SYT6	148281	hgsc.bcm.edu	37	1	114680540	114680540	+	Silent	SNP	C	C	T	rs17032441	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr1:114680540C>T	ENST00000610222.1	-	3	794	c.648G>A	c.(646-648)tcG>tcA	p.S216S	SYT6_ENST00000369547.1_Silent_p.S131S|SYT6_ENST00000607941.1_Silent_p.S131S|SYT6_ENST00000393296.1_Silent_p.S216S|SYT6_ENST00000609117.1_Silent_p.S131S			Q5T7P8	SYT6_HUMAN	synaptotagmin VI	216					acrosomal vesicle exocytosis (GO:0060478)	cell junction (GO:0030054)|cytosol (GO:0005829)|extrinsic component of membrane (GO:0019898)|integral component of membrane (GO:0016021)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	clathrin binding (GO:0030276)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|syntaxin binding (GO:0019905)|transporter activity (GO:0005215)	p.S131S(1)		central_nervous_system(1)|endometrium(3)|large_intestine(10)|lung(14)|ovary(4)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	37	Lung SC(450;0.184)	all_cancers(81;4.41e-08)|all_epithelial(167;5.18e-08)|all_lung(203;1.58e-05)|Lung NSC(69;2.82e-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)		CCCCATCCACCGACTTCTGCT	0.557													c|||	1040	0.207668	0.2247	0.1628	5008	,	,		21878	0.2579		0.2078	False		,,,				2504	0.1646				p.S131S		Atlas-SNP	.											SYT6,NS,carcinoma,0,1	SYT6	66	1	1	Substitution - coding silent(1)	stomach(1)	c.G393A						PASS	.	T		836,3570	331.5+/-302.0	74,688,1441	116.0	101.0	106.0		393	-10.8	0.4	1	dbSNP_123	106	1817,6783	327.6+/-317.9	191,1435,2674	no	coding-synonymous	SYT6	NM_205848.2		265,2123,4115	TT,TC,CC		21.1279,18.9741,20.3983		131/426	114680540	2653,10353	2203	4300	6503	SO:0001819	synonymous_variant	148281	exon3			ATCCACCGACTTC		CCDS871.1	1p13.1	2013-01-21			ENSG00000134207	ENSG00000134207		"""Synaptotagmins"""	18638	protein-coding gene	gene with protein product		607718				11543631	Standard	NM_205848		Approved		uc021orz.1	Q5T7P8	OTTHUMG00000011755	ENST00000610222.1:c.648G>A	1.37:g.114680540C>T		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	71	6	0.084507	NM_205848	B1AMB8|B3KPK1	Silent	SNP	ENST00000610222.1	37																																																																																				.	.	alt		0.557	SYT6-004	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000314819.2	NM_205848	
CWF19L1	55280	hgsc.bcm.edu	37	10	102016044	102016044	+	Missense_Mutation	SNP	C	C	T	rs2270962	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr10:102016044C>T	ENST00000354105.4	-	5	565	c.479G>A	c.(478-480)tGt>tAt	p.C160Y	RNU6-422P_ENST00000384632.1_RNA|CWF19L1_ENST00000478047.1_5'Flank	NM_018294.4	NP_060764.3	Q69YN2	C19L1_HUMAN	CWF19-like 1, cell cycle control (S. pombe)	160			C -> Y (in dbSNP:rs2270962).				catalytic activity (GO:0003824)	p.C160Y(1)		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)		GTTCCCCACACACTTGGGCCA	0.423													T|||	1257	0.250998	0.5998	0.1311	5008	,	,		18538	0.1419		0.0775	False		,,,				2504	0.1554				p.C160Y		Atlas-SNP	.											CWF19L1,NS,carcinoma,0,1	CWF19L1	39	1	1	Substitution - Missense(1)	stomach(1)	c.G479A						scavenged	.	T	TYR/CYS	2270,2136	579.1+/-384.8	590,1090,523	129.0	121.0	124.0		479	4.8	1.0	10	dbSNP_100	124	569,8031	793.7+/-407.5	19,531,3750	yes	missense	CWF19L1	NM_018294.4	194	609,1621,4273	TT,TC,CC		6.6163,48.4793,21.8284	benign	160/539	102016044	2839,10167	2203	4300	6503	SO:0001583	missense	55280	exon5			CCCACACACTTGG	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.479G>A	10.37:g.102016044C>T	ENSP00000326411:p.Cys160Tyr	Somatic	152	1	0.00657895		WXS	Illumina HiSeq	Phase_I	153	7	0.0457516	NM_018294	B4DHX1|D3DR66|Q5W0I3|Q96HC3|Q9H865|Q9NV13	Missense_Mutation	SNP	ENST00000354105.4	37	CCDS7489.1	475	0.2174908424908425	277	0.5630081300813008	47	0.1298342541436464	84	0.14685314685314685	67	0.08839050131926121	T	11.57	1.677721	0.29783	0.515207	0.066163	ENSG00000095485	ENST00000354105	T	0.27402	1.67	6.16	4.85	0.62838	.	0.261247	0.44483	N	0.000453	T	0.00012	0.0000	N	0.01352	-0.895	0.52501	P	4.499999999996174E-5	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.39502	-0.9611	9	0.32370	T	0.25	-3.1421	9.637	0.39814	0.0:0.1624:0.0:0.8376	rs2270962;rs52822289;rs59268290;rs2270962	23;160	Q69YN2-3;Q69YN2	.;C19L1_HUMAN	Y	160	ENSP00000326411:C160Y	ENSP00000326411:C160Y	C	-	2	0	CWF19L1	102006034	0.996000	0.38824	0.998000	0.56505	0.940000	0.58332	1.883000	0.39658	1.152000	0.42452	-0.269000	0.10298	TGT	C|0.775;T|0.225	0.225	strong		0.423	CWF19L1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_018294	
RBM19	9904	hgsc.bcm.edu	37	12	114377885	114377885	+	Silent	SNP	G	G	C	rs2290790	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr12:114377885G>C	ENST00000545145.2	-	15	1896	c.1818C>G	c.(1816-1818)acC>acG	p.T606T	RP11-780K2.1_ENST00000550206.1_RNA|RBM19_ENST00000261741.5_Silent_p.T606T|RBM19_ENST00000392561.3_Silent_p.T606T	NM_001146699.1	NP_001140171.1	Q9Y4C8	RBM19_HUMAN	RNA binding motif protein 19	606	RRM 4. {ECO:0000255|PROSITE- ProRule:PRU00176}.				multicellular organismal development (GO:0007275)|positive regulation of embryonic development (GO:0040019)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(10)|liver(1)|lung(22)|ovary(1)|skin(3)|stomach(4)	55	Medulloblastoma(191;0.163)|all_neural(191;0.178)					AATGGCCGAAGGTCTCCTGCA	0.632													G|||	1099	0.219449	0.0688	0.2565	5008	,	,		17610	0.1756		0.3191	False		,,,				2504	0.3395				p.T606T		Atlas-SNP	.											.	RBM19	117	.	0			c.C1818G						PASS	.	G	,,	469,3937	221.0+/-238.3	31,407,1765	67.0	72.0	70.0		1818,1818,1818	0.1	0.2	12	dbSNP_100	70	2825,5775	441.5+/-359.8	470,1885,1945	no	coding-synonymous,coding-synonymous,coding-synonymous	RBM19	NM_001146698.1,NM_001146699.1,NM_016196.3	,,	501,2292,3710	CC,CG,GG		32.8488,10.6446,25.3268	,,	606/961,606/961,606/961	114377885	3294,9712	2203	4300	6503	SO:0001819	synonymous_variant	9904	exon15			GCCGAAGGTCTCC	AL117547	CCDS9172.1	12q24.21	2013-02-12				ENSG00000122965		"""RNA binding motif (RRM) containing"""	29098	protein-coding gene	gene with protein product						9734811, 11230166	Standard	NM_016196		Approved	DKFZp586F1023, KIAA0682	uc009zwi.2	Q9Y4C8	OTTHUMG00000169646	ENST00000545145.2:c.1818C>G	12.37:g.114377885G>C		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	90	4	0.0444444	NM_001146699	A8K5X9|Q9BPY6|Q9UFN5	Silent	SNP	ENST00000545145.2	37	CCDS9172.1																																																																																			G|0.761;C|0.239	0.239	strong		0.632	RBM19-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405251.1	NM_016196	
ADAMTS14	140766	hgsc.bcm.edu	37	10	72503344	72503344	+	Silent	SNP	G	G	A	rs10999502	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr10:72503344G>A	ENST00000373207.1	+	13	1965	c.1965G>A	c.(1963-1965)acG>acA	p.T655T	ADAMTS14_ENST00000373208.1_Silent_p.T658T	NM_080722.3	NP_542453.2	Q8WXS8	ATS14_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 14	655	Cys-rich.				collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(11)|lung(15)|ovary(7)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	50						CGGCGGACACGGGGGACGTGG	0.622													G|||	1560	0.311502	0.1641	0.2089	5008	,	,		19688	0.5387		0.2167	False		,,,				2504	0.4468				p.T658T		Atlas-SNP	.											ADAMTS14,NS,adenoma,0,1	ADAMTS14	148	1	0			c.G1974A						scavenged	.	G	,	760,3646	308.0+/-290.3	51,658,1494	95.0	76.0	82.0		1965,1974	-10.0	0.4	10	dbSNP_120	82	1824,6776	328.1+/-318.2	192,1440,2668	no	coding-synonymous,coding-synonymous	ADAMTS14	NM_080722.3,NM_139155.2	,	243,2098,4162	AA,AG,GG		21.2093,17.2492,19.8678	,	655/1224,658/1227	72503344	2584,10422	2203	4300	6503	SO:0001819	synonymous_variant	140766	exon13			GGACACGGGGGAC	AF358666	CCDS7306.1, CCDS7307.1	10q21	2008-08-01	2005-08-19		ENSG00000138316	ENSG00000138316		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	14899	protein-coding gene	gene with protein product		607506	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 14"""			11779638	Standard	NM_139155		Approved		uc001jrg.3	Q8WXS8	OTTHUMG00000018414	ENST00000373207.1:c.1965G>A	10.37:g.72503344G>A		Somatic	111	1	0.00900901		WXS	Illumina HiSeq	Phase_I	134	7	0.0522388	NM_139155	Q5T4G0|Q5T4G1|Q8TE55|Q8TEY8	Silent	SNP	ENST00000373207.1	37	CCDS7306.1																																																																																			G|0.768;A|0.232	0.232	strong		0.622	ADAMTS14-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000048522.1	NM_080722	
MUC4	4585	hgsc.bcm.edu	37	3	195510786	195510786	+	Silent	SNP	T	T	G	rs2948677	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr3:195510786T>G	ENST00000463781.3	-	2	8124	c.7665A>C	c.(7663-7665)acA>acC	p.T2555T	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Silent_p.T2555T	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.T2555T(2)		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)		TGGCGTGACCTGTGGATGCTG	0.582													.|||	2649	0.528954	0.4289	0.4524	5008	,	,		13813	0.754		0.5219	False		,,,				2504	0.4939				p.T2555T		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	2	Substitution - coding silent(2)	stomach(2)	c.A7665C						scavenged	.						78.0	65.0	69.0					3																	195510786		678	1591	2269	SO:0001819	synonymous_variant	4585	exon2			GTGACCTGTGGAT	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.7665A>C	3.37:g.195510786T>G		Somatic	118	5	0.0423729		WXS	Illumina HiSeq	Phase_I	130	6	0.0461538	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																																																																																			T|0.500;G|0.500	0.500	strong		0.582	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
SLC22A16	85413	hgsc.bcm.edu	37	6	110778128	110778128	+	Missense_Mutation	SNP	T	T	C	rs714368	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr6:110778128T>C	ENST00000368919.3	-	2	212	c.146A>G	c.(145-147)cAt>cGt	p.H49R	SLC22A16_ENST00000330550.4_Missense_Mutation_p.H47R|SLC22A16_ENST00000456137.2_Missense_Mutation_p.H49R|SLC22A16_ENST00000439654.1_Missense_Mutation_p.H49R|SLC22A16_ENST00000461487.1_5'UTR	NM_033125.3	NP_149116.2	Q86VW1	S22AG_HUMAN	solute carrier family 22 (organic cation/carnitine transporter), member 16	49			H -> R (in dbSNP:rs714368).		acid secretion (GO:0046717)|amine transport (GO:0015837)|carnitine transmembrane transport (GO:1902603)|carnitine transport (GO:0015879)|cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|organic cation transport (GO:0015695)|single fertilization (GO:0007338)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	amine transmembrane transporter activity (GO:0005275)|carnitine transmembrane transporter activity (GO:0015226)|organic cation transmembrane transporter activity (GO:0015101)			breast(1)|endometrium(1)|kidney(3)|large_intestine(6)|lung(16)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	34		all_cancers(87;0.00221)|Acute lymphoblastic leukemia(125;2.27e-07)|all_hematologic(75;1.38e-05)|all_epithelial(87;0.0485)|Colorectal(196;0.101)		OV - Ovarian serous cystadenocarcinoma(136;0.0513)|Epithelial(106;0.0921)|all cancers(137;0.115)	Doxorubicin(DB00997)|L-Carnitine(DB00583)	GCAGACATGATGAGGGGTGAC	0.493													t|||	1572	0.313898	0.3888	0.2406	5008	,	,		17832	0.4097		0.2207	False		,,,				2504	0.2618				p.H49R		Atlas-SNP	.											.	SLC22A16	81	.	0			c.A146G						PASS	.	T	ARG/HIS	1600,2806	496.9+/-363.7	281,1038,884	65.0	68.0	67.0		146	-3.1	0.0	6	dbSNP_86	67	1917,6683	340.3+/-323.5	180,1557,2563	yes	missense	SLC22A16	NM_033125.2	29	461,2595,3447	CC,CT,TT		22.2907,36.3141,27.0414	benign	49/578	110778128	3517,9489	2203	4300	6503	SO:0001583	missense	85413	exon2			ACATGATGAGGGG		CCDS5084.1	6q21	2013-05-22	2008-01-11		ENSG00000004809	ENSG00000004809		"""Solute carriers"""	20302	protein-coding gene	gene with protein product		608276	"""solute carrier family 22 (organic cation transporter), member 16"""			12372408, 12089149, 17473959	Standard	NM_033125		Approved	FLIPT2, CT2, OKB1, OAT6	uc003puf.3	Q86VW1	OTTHUMG00000016171	ENST00000368919.3:c.146A>G	6.37:g.110778128T>C	ENSP00000357915:p.His49Arg	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	88	4	0.0454545	NM_033125	O14567|Q5JXM1|Q8IUG8|Q8IZD5|Q96M90|Q96RU0	Missense_Mutation	SNP	ENST00000368919.3	37	CCDS5084.1	667	0.30540293040293043	172	0.34959349593495936	93	0.2569060773480663	245	0.42832167832167833	157	0.20712401055408972	t	8.623	0.891879	0.17613	0.363141	0.222907	ENSG00000004809	ENST00000368919;ENST00000330550;ENST00000439654;ENST00000437378;ENST00000456137;ENST00000424139	D;T;D;T;D;T	0.82167	-1.58;-0.08;-1.58;-0.08;-1.58;-0.08	4.63	-3.12	0.05282	.	1.299300	0.05397	N	0.540040	T	0.41373	0.1156	N	0.03608	-0.345	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.03453	-1.1035	9	0.27082	T	0.32	.	10.625	0.45502	0.0:0.284:0.0:0.716	rs714368;rs52825948;rs60832844;rs714368	49;47	Q86VW1;Q86VW1-2	S22AG_HUMAN;.	R	49;47;49;6;49;6	ENSP00000357915:H49R;ENSP00000328583:H47R;ENSP00000408799:H49R;ENSP00000416310:H6R;ENSP00000402111:H49R;ENSP00000401007:H6R	ENSP00000328583:H47R	H	-	2	0	SLC22A16	110884821	0.013000	0.17824	0.000000	0.03702	0.002000	0.02628	0.856000	0.27818	-0.837000	0.04223	-1.875000	0.00549	CAT	T|0.701;C|0.299	0.299	strong		0.493	SLC22A16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043428.1	NM_033125	
POLRMT	5442	hgsc.bcm.edu	37	19	619021	619021	+	Silent	SNP	G	G	C	rs14155	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr19:619021G>C	ENST00000588649.2	-	15	3327	c.3243C>G	c.(3241-3243)ccC>ccG	p.P1081P	AC005559.2_ENST00000591847.1_RNA	NM_005035.3	NP_005026.3	O00411	RPOM_HUMAN	polymerase (RNA) mitochondrial (DNA directed)	1081	Mediates interaction with TEFM.				gene expression (GO:0010467)|transcription from mitochondrial promoter (GO:0006390)|transcription initiation from mitochondrial promoter (GO:0006391)	mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|poly(A) RNA binding (GO:0044822)	p.P1081P(1)		cervix(2)|endometrium(3)|large_intestine(1)|lung(9)|ovary(1)|pancreas(2)|prostate(1)|stomach(1)	20		all_epithelial(18;2.78e-22)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;3.55e-06)|all_lung(49;5.41e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		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)		CCAGGCGATAGGGCTGGATGA	0.637													C|||	3117	0.622404	0.7352	0.4006	5008	,	,		13997	0.5823		0.5119	False		,,,				2504	0.7822				p.P1081P		Atlas-SNP	.											POLRMT,colon,carcinoma,0,2	POLRMT	91	2	1	Substitution - coding silent(1)	stomach(1)	c.C3243G						scavenged	.	C		2965,1429		999,967,231	59.0	50.0	53.0		3243	-2.7	1.0	19	dbSNP_52	53	4220,4378		1005,2210,1084	no	coding-synonymous	POLRMT	NM_005035.3		2004,3177,1315	CC,CG,GG		49.0812,32.5216,44.6967		1081/1231	619021	7185,5807	2197	4299	6496	SO:0001819	synonymous_variant	5442	exon15			GCGATAGGGCTGG		CCDS12036.1	19p13.3	2010-10-22			ENSG00000099821	ENSG00000099821	2.7.7.6		9200	protein-coding gene	gene with protein product		601778				9097968	Standard	NM_005035		Approved	h-mtRPOL, APOLMT, MTRNAP, MTRPOL	uc002lpf.1	O00411		ENST00000588649.2:c.3243C>G	19.37:g.619021G>C		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	131	4	0.0305344	NM_005035	O60370	Silent	SNP	ENST00000588649.2	37	CCDS12036.1																																																																																			G|0.442;C|0.558	0.558	strong		0.637	POLRMT-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452172.3	NM_005035	
FAM120B	84498	hgsc.bcm.edu	37	6	170627869	170627869	+	Missense_Mutation	SNP	A	A	G			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr6:170627869A>G	ENST00000476287.1	+	2	1499	c.1391A>G	c.(1390-1392)tAt>tGt	p.Y464C	FAM120B_ENST00000537664.1_Missense_Mutation_p.Y487C|FAM120B_ENST00000540480.1_Missense_Mutation_p.Y476C|FAM120B_ENST00000252510.9_Intron	NM_032448.1	NP_115824.1	Q96EK7	F120B_HUMAN	family with sequence similarity 120B	464					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)		GTTCCCATGTATACAGGCCCT	0.473																																					p.Y464C		Atlas-SNP	.											FAM120B,NS,carcinoma,+1,1	FAM120B	108	1	0			c.A1391G						scavenged	.						158.0	171.0	167.0					6																	170627869		2203	4300	6503	SO:0001583	missense	84498	exon2			CCATGTATACAGG	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.1391A>G	6.37:g.170627869A>G	ENSP00000417970:p.Tyr464Cys	Somatic	170	8	0.0470588		WXS	Illumina HiSeq	Phase_I	160	14	0.0875	NM_032448	B4DL34|Q86V68|Q96JI9	Missense_Mutation	SNP	ENST00000476287.1	37	CCDS5314.1	.	.	.	.	.	.	.	.	.	.	G	0.015	-1.569559	0.00895	.	.	ENSG00000112584	ENST00000540480;ENST00000537664;ENST00000476287	T;T;T	0.07688	3.17;3.17;3.17	2.33	-4.67	0.03319	.	2.051180	0.02593	N	0.100141	T	0.00724	0.0024	N	0.02315	-0.6	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.41574	-0.9501	10	0.36615	T	0.2	.	5.1008	0.14759	0.2586:0.0:0.3377:0.4037	.	464;464	Q96EK7;F2Z2E1	F120B_HUMAN;.	C	476;487;464	ENSP00000444125:Y476C;ENSP00000440125:Y487C;ENSP00000417970:Y464C	ENSP00000436640:Y464C	Y	+	2	0	FAM120B	170469794	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.507000	0.00448	-4.063000	0.00077	-1.462000	0.01023	TAT	.	.	none		0.473	FAM120B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000043259.2	NM_032448	
PER3	8863	hgsc.bcm.edu	37	1	7890024	7890024	+	Missense_Mutation	SNP	T	T	G	rs201662971|rs57875989		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr1:7890024T>G	ENST00000361923.2	+	18	3165	c.2990T>G	c.(2989-2991)aTg>aGg	p.M997R	RP3-467L1.4_ENST00000451646.1_RNA|PER3_ENST00000377532.3_Missense_Mutation_p.M1006R	NM_016831.1	NP_058515.1	P56645	PER3_HUMAN	period circadian clock 3	997	5 X 18 AA tandem repeats of S-[HP]-[AP]- T-[AT]-[GST]-[ATV]-L-S-[MT]-G-[LS]-P-P- [MRS]-[EKR]-[NST]-P.|Ser-rich.				circadian regulation of gene expression (GO:0032922)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of circadian sleep/wake cycle, sleep (GO:0045187)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	signal transducer activity (GO:0004871)	p.M997R(1)		breast(4)|central_nervous_system(3)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(9)|lung(8)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	39	Ovarian(185;0.0634)|all_lung(157;0.178)	all_epithelial(116;9.35e-21)|all_lung(118;7.57e-07)|Lung NSC(185;4.52e-06)|Renal(390;0.000147)|Breast(487;0.00086)|Colorectal(325;0.000959)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0234)|all cancers(8;8.58e-70)|GBM - Glioblastoma multiforme(8;1.81e-35)|Colorectal(212;2.06e-07)|COAD - Colon adenocarcinoma(227;1.92e-05)|Kidney(185;7.18e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000472)|STAD - Stomach adenocarcinoma(132;0.00118)|KIRC - Kidney renal clear cell carcinoma(229;0.00122)|READ - Rectum adenocarcinoma(331;0.0649)		TCGCCTCCCATGAAGAATCCA	0.582																																					p.M997R		Atlas-SNP	.											PER3,NS,carcinoma,0,3	PER3	95	3	1	Substitution - Missense(1)	central_nervous_system(1)	c.T2990G						scavenged	.						85.0	70.0	75.0					1																	7890024		2001	3894	5895	SO:0001583	missense	8863	exon18			CTCCCATGAAGAA	BC026102	CCDS89.1, CCDS72695.1	1p36.23	2012-12-13	2012-12-13		ENSG00000049246	ENSG00000049246			8847	protein-coding gene	gene with protein product		603427	"""period (Drosophila) homolog 3"", ""period homolog 3 (Drosophila)"""			9427249	Standard	XM_005263520		Approved		uc001aoo.3	P56645	OTTHUMG00000001216	ENST00000361923.2:c.2990T>G	1.37:g.7890024T>G	ENSP00000355031:p.Met997Arg	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	63	4	0.0634921	NM_016831	Q5H8X4|Q5H8X5|Q969K6|Q96S77|Q96S78|Q9C0J3|Q9NSP9|Q9UGU8	Missense_Mutation	SNP	ENST00000361923.2	37	CCDS89.1	.	.	.	.	.	.	.	.	.	.	T	0.033	-1.321421	0.01320	.	.	ENSG00000049246	ENST00000377532;ENST00000361923	T;T	0.14640	2.49;2.49	.	.	.	Period circadian-like, C-terminal (1);	31.945600	0.01768	N	0.031022	T	0.04861	0.0131	N	0.04508	-0.205	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	0.25152	-1.0140	8	0.11485	T	0.65	.	.	.	.	.	997;1006;1006;997	A2I2N5;A6H8X0;P56645-2;P56645	.;.;.;PER3_HUMAN	R	1006;997	ENSP00000366755:M1006R;ENSP00000355031:M997R	ENSP00000355031:M997R	M	+	2	0	PER3	7812611	0.004000	0.15560	0.012000	0.15200	0.013000	0.08279	-1.043000	0.03535	-1.402000	0.02056	-1.459000	0.01027	ATG	.	.	weak		0.582	PER3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000003607.1	NM_016831	
ARHGEF2	9181	hgsc.bcm.edu	37	1	155920171	155920171	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr1:155920171G>A	ENST00000361247.4	-	21	2905	c.2806C>T	c.(2806-2808)Cgg>Tgg	p.R936W	ARHGEF2_ENST00000368315.4_Missense_Mutation_p.R937W|ARHGEF2_ENST00000462460.2_Missense_Mutation_p.R981W|ARHGEF2_ENST00000313667.4_Missense_Mutation_p.R935W|ARHGEF2_ENST00000368316.1_Missense_Mutation_p.R908W|ARHGEF2_ENST00000313695.7_Missense_Mutation_p.R908W|ARHGEF2_ENST00000477754.2_Intron	NM_001162383.1|NM_001162384.1	NP_001155855.1|NP_001155856.1	Q92974	ARHG2_HUMAN	Rho/Rac guanine nucleotide exchange factor (GEF) 2	936					actin filament organization (GO:0007015)|apoptotic signaling pathway (GO:0097190)|cell morphogenesis (GO:0000902)|cellular hyperosmotic response (GO:0071474)|cellular response to muramyl dipeptide (GO:0071225)|cellular response to tumor necrosis factor (GO:0071356)|establishment of mitotic spindle orientation (GO:0000132)|innate immune response (GO:0045087)|intracellular protein transport (GO:0006886)|mitotic nuclear division (GO:0007067)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of intrinsic apoptotic signaling pathway in response to osmotic stress (GO:1902219)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of necroptotic process (GO:0060546)|negative regulation of neurogenesis (GO:0050768)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|regulation of cell proliferation (GO:0042127)|regulation of Rho protein signal transduction (GO:0035023)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|neuronal cell body (GO:0043025)|protein complex (GO:0043234)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)|vesicle (GO:0031982)	microtubule binding (GO:0008017)|Rac GTPase binding (GO:0048365)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|Rho GTPase binding (GO:0017048)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			breast(4)|cervix(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(6)|lung(15)|ovary(1)|skin(2)	40	Hepatocellular(266;0.133)|all_hematologic(923;0.145)|all_neural(408;0.195)					TCTTGCAGCCGCTCTTCGGGG	0.627																																					p.R936W	Melanoma(178;35 2768 6610 28839)	Atlas-SNP	.											.	ARHGEF2	81	.	0			c.C2806T						PASS	.						58.0	55.0	56.0					1																	155920171		2203	4300	6503	SO:0001583	missense	9181	exon21			GCAGCCGCTCTTC	AB014551	CCDS1125.1, CCDS53375.1, CCDS53376.1	1q21-q22	2013-01-10	2009-06-12		ENSG00000116584	ENSG00000116584		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	682	protein-coding gene	gene with protein product		607560	"""rho/rac guanine nucleotide exchange factor (GEF) 2"""			9857026, 9734811	Standard	NM_004723		Approved	LFP40, GEF-H1, KIAA0651, P40	uc001fmt.2	Q92974	OTTHUMG00000017464	ENST00000361247.4:c.2806C>T	1.37:g.155920171G>A	ENSP00000354837:p.Arg936Trp	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	72	16	0.222222	NM_001162383	D3DVA6|O75142|Q15079|Q5VY92|Q8TDA3|Q8WUG4|Q9H023	Missense_Mutation	SNP	ENST00000361247.4	37	CCDS53376.1	.	.	.	.	.	.	.	.	.	.	G	13.65	2.300726	0.40694	.	.	ENSG00000116584	ENST00000313695;ENST00000361247;ENST00000368315;ENST00000368316;ENST00000313667	T;T;T;T;T	0.69561	-0.4;-0.28;-0.29;-0.4;-0.41	5.98	5.06	0.68205	.	0.177972	0.27319	N	0.019911	T	0.42877	0.1222	N	0.19112	0.55	0.33849	D	0.632384	D;P;P;D	0.60575	0.975;0.916;0.95;0.988	B;B;P;B	0.46275	0.312;0.312;0.51;0.386	T	0.54111	-0.8342	10	0.62326	D	0.03	-22.727	12.5577	0.56263	0.0:0.0:0.8335:0.1665	.	980;936;935;937	D3DVA5;Q92974;Q92974-2;Q5VY93	.;ARHG2_HUMAN;.;.	W	908;936;937;908;935	ENSP00000315325:R908W;ENSP00000354837:R936W;ENSP00000357298:R937W;ENSP00000357299:R908W;ENSP00000314787:R935W	ENSP00000314787:R935W	R	-	1	2	ARHGEF2	154186795	1.000000	0.71417	0.973000	0.42090	0.242000	0.25591	4.760000	0.62235	1.518000	0.48934	-0.181000	0.13052	CGG	.	.	none		0.627	ARHGEF2-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046204.2	NM_004723	
MAGEB16	139604	hgsc.bcm.edu	37	X	35821127	35821127	+	Nonsense_Mutation	SNP	C	C	T	rs4829392	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chrX:35821127C>T	ENST00000399989.1	+	2	1093	c.814C>T	c.(814-816)Cga>Tga	p.R272*	MAGEB16_ENST00000399988.1_Nonsense_Mutation_p.R272*|MAGEB16_ENST00000399987.1_Nonsense_Mutation_p.R272*|MAGEB16_ENST00000399992.1_Nonsense_Mutation_p.R304*|MAGEB16_ENST00000399985.1_Nonsense_Mutation_p.R272*	NM_001099921.1	NP_001093391.1	A2A368	MAGBG_HUMAN	melanoma antigen family B, 16	272	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.									breast(2)|endometrium(1)|kidney(2)|large_intestine(2)|lung(16)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	31						TGATCCTGCACGATATGAATT	0.483													C|||	2342	0.620397	0.4478	0.4121	3775	,	,		15380	0.5694		0.4195	False		,,,				2504	0.4785				p.R272X		Atlas-SNP	.											.	MAGEB16	64	.	0			c.C814T						PASS	.	C	stop/ARG	2170,1655		540,782,308,305,263	38.0	38.0	38.0		814	-1.3	0.0	X	dbSNP_111	38	3581,3147		694,1206,987,528,885	yes	stop-gained	MAGEB16	NM_001099921.1		1234,1988,1295,833,1148	TT,TC,T,CC,C		46.7747,43.268,45.5036		272/325	35821127	5751,4802	2198	4300	6498	SO:0001587	stop_gained	139604	exon2			CCTGCACGATATG		CCDS43927.1	Xp21.1	2010-05-26	2005-11-07		ENSG00000189023	ENSG00000189023			21188	protein-coding gene	gene with protein product		300762	"""melanoma antigen family B, 16 (pseudogene)"""			11454705	Standard	NM_001099921		Approved		uc010ngt.1	A2A368	OTTHUMG00000021348	ENST00000399989.1:c.814C>T	X.37:g.35821127C>T	ENSP00000382871:p.Arg272*	Somatic	357	0	0		WXS	Illumina HiSeq	Phase_I	320	13	0.040625	NM_001099921	A8MU30	Nonsense_Mutation	SNP	ENST00000399989.1	37	CCDS43927.1	1014	0.6112115732368897	151	0.4415204678362573	102	0.4146341463414634	212	0.5792349726775956	230	0.3885135135135135	C	16.21	3.060037	0.55325	0.56732	0.532253	ENSG00000189023	ENST00000399988;ENST00000399992;ENST00000399987;ENST00000399989;ENST00000399985	.	.	.	3.13	-1.27	0.09347	.	0.391845	0.25596	N	0.029598	.	.	.	.	.	.	0.09310	P	0.99999629397	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	5.9248	0.19104	0.5383:0.2869:0.1748:0.0	rs4829392;rs52830693;rs4829392	.	.	.	X	272;304;272;272;272	.	ENSP00000382867:R272X	R	+	1	2	MAGEB16	35731048	0.000000	0.05858	0.000000	0.03702	0.404000	0.30871	0.056000	0.14256	-0.423000	0.07394	-0.340000	0.08031	CGA	C|0.356;0|0.042	.	strong		0.483	MAGEB16-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251034.1		
DDR1	780	hgsc.bcm.edu	37	6	30864829	30864829	+	Silent	SNP	T	T	C	rs1049623	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr6:30864829T>C	ENST00000324771.8	+	16	2456	c.1908T>C	c.(1906-1908)gtT>gtC	p.V636V	DDR1_ENST00000452441.1_Silent_p.V636V|DDR1_ENST00000376575.3_Silent_p.V636V|DDR1_ENST00000418800.2_Silent_p.V599V|DDR1_ENST00000376568.3_Silent_p.V636V|DDR1_ENST00000446312.1_3'UTR|DDR1_ENST00000508312.1_Silent_p.V617V|DDR1_ENST00000513240.1_Silent_p.V636V|DDR1_ENST00000376567.2_Silent_p.V599V|DDR1_ENST00000376570.4_Silent_p.V599V|DDR1_ENST00000454612.2_Silent_p.V599V|DDR1_ENST00000376569.3_Silent_p.V599V|DDR1_ENST00000361741.4_Silent_p.V303V			Q08345	DDR1_HUMAN	discoidin domain receptor tyrosine kinase 1	636	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				branching involved in mammary gland duct morphogenesis (GO:0060444)|cell adhesion (GO:0007155)|collagen-activated tyrosine kinase receptor signaling pathway (GO:0038063)|ear development (GO:0043583)|embryo implantation (GO:0007566)|extracellular matrix organization (GO:0030198)|lactation (GO:0007595)|mammary gland alveolus development (GO:0060749)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine autophosphorylation (GO:0038083)|protein autophosphorylation (GO:0046777)|regulation of cell growth (GO:0001558)|regulation of cell-matrix adhesion (GO:0001952)|regulation of extracellular matrix disassembly (GO:0010715)|smooth muscle cell migration (GO:0014909)|smooth muscle cell-matrix adhesion (GO:0061302)|wound healing, spreading of cells (GO:0044319)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|collagen binding (GO:0005518)|metal ion binding (GO:0046872)|protein tyrosine kinase collagen receptor activity (GO:0038062)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			central_nervous_system(3)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(14)|ovary(1)|prostate(1)|skin(1)	29					Imatinib(DB00619)	AAGATCTGGTTAGTCTTGATT	0.512													C|||	2683	0.535743	0.4531	0.5245	5008	,	,		14894	0.6667		0.3847	False		,,,				2504	0.6759				p.V636V		Atlas-SNP	.											DDR1_ENST00000376575,NS,adenoma,0,3	DDR1	213	3	0			c.T1908C	GRCh37	CM076148	DDR1	M	rs1049623	PASS	.	C	,,,,,	2008,2398	615.9+/-392.7	473,1062,668	203.0	181.0	189.0		,1470,1851,1797,1908,1908	5.3	1.0	6	dbSNP_86	189	3287,5313	648.3+/-400.5	620,2047,1633	no	utr-3,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	DDR1	NM_001202521.1,NM_001202522.1,NM_001202523.1,NM_001954.4,NM_013993.2,NM_013994.2	,,,,,	1093,3109,2301	CC,CT,TT		38.2209,45.5742,40.712	,,,,,	,490/768,617/895,599/877,636/914,636/920	30864829	5295,7711	2203	4300	6503	SO:0001819	synonymous_variant	780	exon13			TCTGGTTAGTCTT	X99031	CCDS4690.1, CCDS34385.1, CCDS47396.1, CCDS56411.1, CCDS75419.1	6p21.33	2010-02-17	2008-01-23		ENSG00000204580	ENSG00000204580	2.7.10.1	"""CD molecules"""	2730	protein-coding gene	gene with protein product		600408	"""discoidin domain receptor family, member 1"""	NTRK4, PTK3A, NEP, CAK, EDDR1		7789998	Standard	NM_001954		Approved	RTK6, CD167	uc003nrv.3	Q08345	OTTHUMG00000031236	ENST00000324771.8:c.1908T>C	6.37:g.30864829T>C		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	158	7	0.0443038	NM_013994	B5A975|B5A976|B7Z2K0|Q14196|Q16562|Q2L6H3|Q4LE50|Q5ST11|Q5ST12|Q6NSK4|Q9UD35|Q9UD36|Q9UD37|Q9UD86|Q9UDL2	Silent	SNP	ENST00000324771.8	37	CCDS34385.1	1109	0.5077838827838828	252	0.5121951219512195	189	0.5220994475138122	349	0.6101398601398601	319	0.420844327176781	C	10.41	1.343892	0.24339	0.455742	0.382209	ENSG00000204580	ENST00000514434	.	.	.	5.29	5.29	0.74685	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	0.9999999999999912	.	.	.	.	.	.	.	.	.	.	.	.	.	.	7.79	0.29114	0.0:0.7501:0.1626:0.0873	rs1049623;rs1264316;rs2228636;rs3173380;rs17413087;rs58133601;rs1049623	.	.	.	Q	128	.	.	X	+	1	0	DDR1	30972808	0.012000	0.17670	1.000000	0.80357	0.871000	0.50021	0.586000	0.23894	1.250000	0.43966	-0.215000	0.12644	TAG	T|0.539;C|0.461	0.461	strong		0.512	DDR1-005	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076494.3	NM_013994	
LRRC47	57470	hgsc.bcm.edu	37	1	3703710	3703710	+	Silent	SNP	G	G	A	rs2253143	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr1:3703710G>A	ENST00000378251.1	-	2	807	c.780C>T	c.(778-780)gtC>gtT	p.V260V	RP1-286D6.5_ENST00000607459.1_RNA	NM_020710.2	NP_065761.1	Q8N1G4	LRC47_HUMAN	leucine rich repeat containing 47	260							phenylalanine-tRNA ligase activity (GO:0004826)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(5)|ovary(2)|prostate(1)|urinary_tract(1)	17	all_cancers(77;0.0375)|Ovarian(185;0.0634)|all_lung(157;0.208)|Lung NSC(156;0.21)	all_epithelial(116;1.34e-16)|all_lung(118;2.53e-06)|Lung NSC(185;0.00028)|Renal(390;0.00357)|Breast(487;0.00446)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Lung SC(97;0.0743)|Ovarian(437;0.127)		Epithelial(90;5.49e-39)|OV - Ovarian serous cystadenocarcinoma(86;1.43e-22)|GBM - Glioblastoma multiforme(42;3.69e-16)|Colorectal(212;1.21e-05)|COAD - Colon adenocarcinoma(227;5.87e-05)|Kidney(185;0.000367)|BRCA - Breast invasive adenocarcinoma(365;0.000704)|KIRC - Kidney renal clear cell carcinoma(229;0.00567)|STAD - Stomach adenocarcinoma(132;0.00645)|Lung(427;0.124)		CACGGCCTCCGACGCGCAGGT	0.632													G|||	467	0.0932508	0.0068	0.111	5008	,	,		17403	0.2837		0.0318	False		,,,				2504	0.0644				p.V260V		Atlas-SNP	.											.	LRRC47	42	.	0			c.C780T						PASS	.	G		51,4355	51.6+/-87.1	0,51,2152	73.0	60.0	65.0		780	-8.5	0.0	1	dbSNP_100	65	210,8390	89.2+/-151.4	6,198,4096	no	coding-synonymous	LRRC47	NM_020710.2		6,249,6248	AA,AG,GG		2.4419,1.1575,2.0068		260/584	3703710	261,12745	2203	4300	6503	SO:0001819	synonymous_variant	57470	exon2			GCCTCCGACGCGC	AB033011	CCDS51.1	1p36.32	2008-02-05			ENSG00000130764	ENSG00000130764			29207	protein-coding gene	gene with protein product						10574461	Standard	NM_020710		Approved	KIAA1185, RP1-286D6.3	uc001akx.1	Q8N1G4	OTTHUMG00000003506	ENST00000378251.1:c.780C>T	1.37:g.3703710G>A		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	66	5	0.0757576	NM_020710	Q9ULN5	Silent	SNP	ENST00000378251.1	37	CCDS51.1																																																																																			G|0.949;A|0.051	0.051	strong		0.632	LRRC47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009744.1	NM_020710	
MMP8	4317	hgsc.bcm.edu	37	11	102587062	102587062	+	Silent	SNP	G	G	A	rs3740938	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr11:102587062G>A	ENST00000236826.3	-	6	971	c.873C>T	c.(871-873)ctC>ctT	p.L291L		NM_002424.2	NP_002415.1	P22894	MMP8_HUMAN	matrix metallopeptidase 8 (neutrophil collagenase)	291					collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|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)|metalloendopeptidase activity (GO:0004222)|serine-type endopeptidase activity (GO:0004252)|zinc ion binding (GO:0008270)	p.L291L(1)		autonomic_ganglia(1)|breast(3)|kidney(1)|large_intestine(4)|lung(11)|ovary(4)|skin(6)|stomach(1)|urinary_tract(1)	32	all_cancers(8;0.00092)|all_epithelial(12;0.00389)|Lung NSC(15;0.227)	all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)	Epithelial(9;0.0555)|Lung(13;0.0828)|LUSC - Lung squamous cell carcinoma(19;0.151)|all cancers(10;0.189)	BRCA - Breast invasive adenocarcinoma(274;0.0141)	Marimastat(DB00786)	TTTCTCCACGGAGTGTGGTGA	0.378													G|||	588	0.117412	0.0038	0.1282	5008	,	,		16940	0.2778		0.0626	False		,,,				2504	0.1544				p.L291L		Atlas-SNP	.											MMP8,colon,carcinoma,0,5	MMP8	68	5	1	Substitution - coding silent(1)	stomach(1)	c.C873T						scavenged	.	G		86,4320	71.4+/-109.4	3,80,2120	117.0	122.0	120.0		873	4.1	1.0	11	dbSNP_107	120	547,8051	151.0+/-205.8	15,517,3767	no	coding-synonymous	MMP8	NM_002424.2		18,597,5887	AA,AG,GG		6.3619,1.9519,4.8677		291/468	102587062	633,12371	2203	4299	6502	SO:0001819	synonymous_variant	4317	exon6			TCCACGGAGTGTG	J05556	CCDS8320.1	11q21-q22	2008-02-05	2005-08-08		ENSG00000118113	ENSG00000118113	3.4.24.34		7175	protein-coding gene	gene with protein product		120355	"""matrix metalloproteinase 8 (neutrophil collagenase)"""	CLG1			Standard	NM_002424		Approved		uc001phe.2	P22894	OTTHUMG00000167587	ENST00000236826.3:c.873C>T	11.37:g.102587062G>A		Somatic	232	0	0		WXS	Illumina HiSeq	Phase_I	242	8	0.0330578	NM_002424	Q45F99	Silent	SNP	ENST00000236826.3	37	CCDS8320.1	241	0.11034798534798534	1	0.0020325203252032522	40	0.11049723756906077	155	0.270979020979021	45	0.059366754617414245	G	8.669	0.902281	0.17760	0.019519	0.063619	ENSG00000118113	ENST00000438475	.	.	.	5.03	4.11	0.48088	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999495	.	.	.	.	.	.	T	0.17258	-1.0375	3	.	.	.	.	8.5229	0.33287	0.0:0.1684:0.6573:0.1743	rs3740938;rs60162198;rs3740938	.	.	.	S	267	.	.	P	-	1	0	MMP8	102092272	0.632000	0.27172	0.990000	0.47175	0.986000	0.74619	-0.270000	0.08584	1.092000	0.41356	0.563000	0.77884	CCG	G|0.920;A|0.080	0.080	strong		0.378	MMP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395223.1	NM_002424	
LAMA3	3909	hgsc.bcm.edu	37	18	21394444	21394444	+	Missense_Mutation	SNP	A	A	C			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr18:21394444A>C	ENST00000313654.9	+	15	2107	c.1866A>C	c.(1864-1866)aaA>aaC	p.K622N	LAMA3_ENST00000399516.3_Missense_Mutation_p.K622N	NM_198129.1	NP_937762.1	Q16787	LAMA3_HUMAN	laminin, alpha 3	622	Domain V.|Laminin EGF-like 6. {ECO:0000255|PROSITE- ProRule:PRU00460}.				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)					ATCTGGACAAAGAAAACCCCA	0.363																																					p.K622N		Atlas-SNP	.											.	LAMA3	397	.	0			c.A1866C						PASS	.						140.0	129.0	132.0					18																	21394444		1812	4088	5900	SO:0001583	missense	3909	exon15			GGACAAAGAAAAC	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.1866A>C	18.37:g.21394444A>C	ENSP00000324532:p.Lys622Asn	Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	139	52	0.374101	NM_001127717	B0YJ33|Q13679|Q13680|Q6VU67|Q6VU68|Q6VU69|Q76E14|Q96TG0	Missense_Mutation	SNP	ENST00000313654.9	37	CCDS42419.1	.	.	.	.	.	.	.	.	.	.	A	11.46	1.645160	0.29246	.	.	ENSG00000053747	ENST00000313654;ENST00000399516;ENST00000416669	T;T	0.54071	0.59;0.59	5.64	0.566	0.17317	EGF-like, laminin (3);	.	.	.	.	T	0.42381	0.1200	M	0.72118	2.19	0.80722	D	1	P;P	0.36392	0.551;0.551	B;B	0.31390	0.084;0.129	T	0.21484	-1.0244	9	0.21014	T	0.42	.	6.9004	0.24279	0.6634:0.1273:0.2093:0.0	.	622;622	Q6VU67;Q16787	.;LAMA3_HUMAN	N	622;622;620	ENSP00000324532:K622N;ENSP00000382432:K622N	ENSP00000324532:K622N	K	+	3	2	LAMA3	19648442	0.055000	0.20627	0.862000	0.33874	0.712000	0.41017	0.579000	0.23788	0.432000	0.26286	-0.256000	0.11100	AAA	.	.	none		0.363	LAMA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254824.3	NM_000227, NM_198129	
MGAM	8972	hgsc.bcm.edu	37	7	141759688	141759688	+	Silent	SNP	T	T	C			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr7:141759688T>C	ENST00000549489.2	+	33	4076	c.3981T>C	c.(3979-3981)ccT>ccC	p.P1327P	MGAM_ENST00000475668.2_Silent_p.P1327P	NM_004668.2	NP_004659.2	O43451	MGA_HUMAN	maltase-glucoamylase (alpha-glucosidase)	1327	Glucoamylase.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)|starch catabolic process (GO:0005983)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|amylase activity (GO:0016160)|carbohydrate binding (GO:0030246)|catalytic activity (GO:0003824)|glucan 1,4-alpha-glucosidase activity (GO:0004339)|maltose alpha-glucosidase activity (GO:0032450)	p.P1327P(2)		cervix(1)|endometrium(1)|large_intestine(4)|lung(3)|ovary(2)|skin(2)	13	Melanoma(164;0.0272)				Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	AGACACAGCCTTATCCTGCCT	0.463																																					p.P1327P		Atlas-SNP	.											MGAM_ENST00000549489,NS,carcinoma,0,5	MGAM	767	5	2	Substitution - coding silent(2)	prostate(2)	c.T3981C						scavenged	.						50.0	43.0	45.0					7																	141759688		1935	4135	6070	SO:0001819	synonymous_variant	8972	exon33			ACAGCCTTATCCT	AF016833	CCDS47727.1	7q34	2012-10-03			ENSG00000257335	ENSG00000257335			7043	protein-coding gene	gene with protein product		154360				9446624	Standard	NM_004668		Approved	MGA	uc003vwy.3	O43451	OTTHUMG00000158395	ENST00000549489.2:c.3981T>C	7.37:g.141759688T>C		Somatic	169	5	0.0295858		WXS	Illumina HiSeq	Phase_I	169	4	0.0236686	NM_004668	Q0VAX6|Q75ME7|Q86UM5	Silent	SNP	ENST00000549489.2	37	CCDS47727.1																																																																																			.	.	none		0.463	MGAM-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000351244.3		
ARMC5	79798	hgsc.bcm.edu	37	16	31473872	31473872	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr16:31473872G>A	ENST00000563544.1	+	4	1550	c.1004G>A	c.(1003-1005)cGg>cAg	p.R335Q	ARMC5_ENST00000538189.1_Missense_Mutation_p.R367Q|ARMC5_ENST00000408912.3_Missense_Mutation_p.R430Q|ARMC5_ENST00000268314.4_Missense_Mutation_p.R335Q|ARMC5_ENST00000412665.2_Intron|ARMC5_ENST00000457010.2_Missense_Mutation_p.R335Q|RP11-452L6.5_ENST00000564629.1_RNA			Q96C12	ARMC5_HUMAN	armadillo repeat containing 5	335										central_nervous_system(1)|endometrium(4)|large_intestine(3)|liver(2)|lung(12)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	28						CGGCAGCGCCGGGATCCTAAT	0.647																																					p.R335Q		Atlas-SNP	.											ARMC5_ENST00000457010,NS,carcinoma,+1,2	ARMC5	94	2	0			c.G1004A						PASS	.						36.0	41.0	39.0					16																	31473872		1998	4168	6166	SO:0001583	missense	79798	exon3			AGCGCCGGGATCC	AY217348	CCDS42155.1, CCDS45472.1, CCDS73874.1	16p11	2013-02-14			ENSG00000140691	ENSG00000140691		"""Armadillo repeat containing"""	25781	protein-coding gene	gene with protein product		615549					Standard	NM_024742		Approved	FLJ13063	uc002ecc.3	Q96C12	OTTHUMG00000176618	ENST00000563544.1:c.1004G>A	16.37:g.31473872G>A	ENSP00000456877:p.Arg335Gln	Somatic	17	0	0		WXS	Illumina HiSeq	Phase_I	26	10	0.384615	NM_024742	Q86WM9|Q9H7P8|Q9H925	Missense_Mutation	SNP	ENST00000563544.1	37	CCDS45472.1	.	.	.	.	.	.	.	.	.	.	g	13.89	2.371251	0.42003	.	.	ENSG00000140691	ENST00000408912;ENST00000538189;ENST00000268314;ENST00000457010	T;T;T;T	0.22743	1.94;1.94;1.94;1.94	4.8	4.8	0.61643	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.53938	D	0.000055	T	0.31009	0.0783	L	0.34521	1.04	0.80722	D	1	D;D;D;D	0.71674	0.998;0.998;0.998;0.998	D;D;D;P	0.72982	0.979;0.979;0.979;0.895	T	0.02596	-1.1136	10	0.15066	T	0.55	-5.4148	13.3511	0.60603	0.0:0.0:1.0:0.0	.	367;430;335;335	F5H156;B4DIU9;Q96C12;Q96C12-4	.;.;ARMC5_HUMAN;.	Q	430;367;335;335	ENSP00000386125:R430Q;ENSP00000443995:R367Q;ENSP00000268314:R335Q;ENSP00000399561:R335Q	ENSP00000268314:R335Q	R	+	2	0	ARMC5	31381373	0.993000	0.37304	0.894000	0.35097	0.044000	0.14063	3.649000	0.54417	2.217000	0.71921	0.457000	0.33378	CGG	.	.	none		0.647	ARMC5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432847.1	NM_024742	
MUC16	94025	hgsc.bcm.edu	37	19	9012826	9012826	+	Missense_Mutation	SNP	T	T	C			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr19:9012826T>C	ENST00000397910.4	-	34	38821	c.38618A>G	c.(38617-38619)cAt>cGt	p.H12873R		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	12875	SEA 6. {ECO:0000255|PROSITE- ProRule:PRU00188}.			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						GCCTGGGTGATGCATGTCCTC	0.587																																					p.H12873R		Atlas-SNP	.											MUC16_ENST00000397910,NS,lymphoid_neoplasm,0,2	MUC16	4315	2	0			c.A38618G						scavenged	.						225.0	191.0	202.0					19																	9012826		2025	4191	6216	SO:0001583	missense	94025	exon34			GGGTGATGCATGT	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.38618A>G	19.37:g.9012826T>C	ENSP00000381008:p.His12873Arg	Somatic	134	1	0.00746269		WXS	Illumina HiSeq	Phase_I	135	5	0.037037	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	.	0.961	-0.703220	0.03255	.	.	ENSG00000181143	ENST00000397910;ENST00000441155	T	0.28666	1.6	1.74	-3.49	0.04724	.	.	.	.	.	T	0.23094	0.0558	.	.	.	.	.	.	B	0.02656	0.0	B	0.01281	0.0	T	0.04737	-1.0930	7	0.87932	D	0	2.498	9.967	0.41730	0.0:0.6375:0.0:0.3625	.	12873	B5ME49	.	R	12873;26	ENSP00000381008:H12873R	ENSP00000381008:H12873R	H	-	2	0	MUC16	8873826	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-6.071000	0.00082	-2.450000	0.00543	-2.166000	0.00325	CAT	.	.	none		0.587	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
TPSD1	23430	hgsc.bcm.edu	37	16	1306346	1306346	+	Missense_Mutation	SNP	C	C	T	rs3865205	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr16:1306346C>T	ENST00000211076.3	+	1	213	c.65C>T	c.(64-66)cCg>cTg	p.P22L	TPSD1_ENST00000397534.2_Missense_Mutation_p.P15L|RP11-616M22.5_ENST00000566997.1_RNA	NM_012217.2	NP_036349.1	Q9BZJ3	TRYD_HUMAN	tryptase delta 1	22			P -> R (in dbSNP:rs3865205). {ECO:0000269|PubMed:9920877}.			extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(9)|skin(1)|stomach(2)|upper_aerodigestive_tract(3)	20		Hepatocellular(780;0.00369)				CTGGCGAGCCCGGCCTACGTG	0.721													-|||	872	0.174121	0.3003	0.2522	5008	,	,		14799	0.123		0.0984	False		,,,				2504	0.0787				p.P22L		Atlas-SNP	.											TPSD1,rectum,carcinoma,0,4	TPSD1	47	4	0			c.C65T						scavenged	.	T	LEU/PRO	1156,3238		166,824,1207	32.0	40.0	37.0		65	0.1	0.0	16	dbSNP_108	37	783,7813		37,709,3552	no	missense	TPSD1	NM_012217.2	98	203,1533,4759	TT,TC,CC		9.1089,26.3086,14.9269	benign	22/243	1306346	1939,11051	2197	4298	6495	SO:0001583	missense	23430	exon1			CGAGCCCGGCCTA	AF206664	CCDS10432.1	16p13.3	2008-07-29			ENSG00000095917	ENSG00000095917	3.4.21.59		14118	protein-coding gene	gene with protein product	"""mMCP-7-like II"", ""mMCP-7-like I"", ""MMCP-7-LIKE-2"""	609272				9920877	Standard	NM_012217		Approved		uc002clb.1	Q9BZJ3	OTTHUMG00000128511	ENST00000211076.3:c.65C>T	16.37:g.1306346C>T	ENSP00000211076:p.Pro22Leu	Somatic	200	0	0		WXS	Illumina HiSeq	Phase_I	209	6	0.0287081	NM_012217	O95824|Q8TDI6|Q96L36|Q96RZ5|Q9H2Y6|Q9UQI8	Missense_Mutation	SNP	ENST00000211076.3	37	CCDS10432.1	379	0.17353479853479853	154	0.3130081300813008	83	0.2292817679558011	75	0.13111888111888112	67	0.08839050131926121	-	6.229	0.410456	0.11812	0.263086	0.091089	ENSG00000095917	ENST00000397534;ENST00000211076	T;T	0.80653	-1.4;-1.4	2.55	0.112	0.14623	.	2.133630	0.02279	N	0.069280	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.05022	-1.0911	9	0.10111	T	0.7	.	6.9607	0.24595	0.0:0.3788:0.0:0.6212	rs3865205;rs3891050	22	Q9BZJ3	TRYD_HUMAN	L	15;22	ENSP00000380668:P15L;ENSP00000211076:P22L	ENSP00000211076:P22L	P	+	2	0	TPSD1	1246347	0.000000	0.05858	0.007000	0.13788	0.001000	0.01503	-2.678000	0.00839	-0.544000	0.06232	-2.646000	0.00150	CCG	C|0.851;T|0.149	0.149	strong		0.721	TPSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250320.2		
CLCNKA	1187	hgsc.bcm.edu	37	1	16351310	16351310	+	Silent	SNP	T	T	C	rs118025694	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr1:16351310T>C	ENST00000331433.4	+	4	301	c.282T>C	c.(280-282)ctT>ctC	p.L94L	CLCNKA_ENST00000375692.1_Silent_p.L94L|CLCNKA_ENST00000439316.2_Intron|CLCNKA_ENST00000464764.1_Intron|CLCNKA_ENST00000420078.1_Silent_p.L94L			P51800	CLCKA_HUMAN	chloride channel, voltage-sensitive Ka	94					excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|regulation of anion transport (GO:0044070)|transmembrane transport (GO:0055085)|transport (GO:0006810)	chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	adenyl nucleotide binding (GO:0030554)|metal ion binding (GO:0046872)|voltage-gated chloride channel activity (GO:0005247)			breast(1)|kidney(1)|large_intestine(2)|lung(12)|ovary(2)|skin(1)	19		Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Colorectal(212;8.04e-08)|COAD - Colon adenocarcinoma(227;5.46e-06)|BRCA - Breast invasive adenocarcinoma(304;9.02e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.00655)|READ - Rectum adenocarcinoma(331;0.0649)	Niflumic Acid(DB04552)	TCCGGTATCTTTCCTGGACTG	0.627													T|||	4	0.000798722	0.0	0.0	5008	,	,		16390	0.004		0.0	False		,,,				2504	0.0				p.L94L		Atlas-SNP	.											CLCNKA,NS,carcinoma,+2,1	CLCNKA	56	1	0			c.T282C						PASS	.						139.0	105.0	116.0					1																	16351310		2203	4300	6503	SO:0001819	synonymous_variant	1187	exon4			GTATCTTTCCTGG		CCDS167.1, CCDS41269.1, CCDS57973.1	1p36	2012-09-26	2012-02-23		ENSG00000186510	ENSG00000186510		"""Ion channels / Chloride channels : Voltage-sensitive"""	2026	protein-coding gene	gene with protein product		602024	"""chloride channel Ka"""			8544406	Standard	NM_004070		Approved	hClC-Ka	uc001axu.3	P51800	OTTHUMG00000009529	ENST00000331433.4:c.282T>C	1.37:g.16351310T>C		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	84	4	0.047619	NM_004070	B4DPD3|E7EPH6|Q5T5P8|Q5T5Q4|Q7Z6D1|Q86VT1	Silent	SNP	ENST00000331433.4	37	CCDS167.1																																																																																			T|0.997;C|0.003	0.003	strong		0.627	CLCNKA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000026326.1		
UBB	7314	hgsc.bcm.edu	37	17	16285491	16285491	+	Silent	SNP	C	C	T	rs16962973		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr17:16285491C>T	ENST00000395837.1	+	2	451	c.270C>T	c.(268-270)acC>acT	p.T90T	UBB_ENST00000302182.3_Silent_p.T90T|RP11-138I1.4_ENST00000583934.1_RNA|UBB_ENST00000578649.1_Intron|UBB_ENST00000395839.1_Silent_p.T90T|UBB_ENST00000535788.1_Intron	NM_001281718.1|NM_001281720.1	NP_001268647.1|NP_001268649.1	P0CG47	UBB_HUMAN	ubiquitin B	90	Ubiquitin-like 2. {ECO:0000255|PROSITE- ProRule:PRU00214}.		GMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQ QRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFV KTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFA GKQLEDGRTLSDYNIQKESTLHLVLRLRGGC -> YADLRE DPDRQDHHPGSGAQ (in UBB(+1); loss of polyubiquitination; impairs the ubiquitin-proteasome pathway; refractory to disassembly by DUBs; slow degradation by UCHL3).		activation of MAPK activity (GO:0000187)|anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|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 peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|carbohydrate metabolic process (GO:0005975)|cellular response to hypoxia (GO:0071456)|cytokine-mediated signaling pathway (GO:0019221)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|endosomal transport (GO:0016197)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|gene expression (GO:0010467)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|innate immune response (GO:0045087)|intracellular transport of virus (GO:0075733)|ion transmembrane transport (GO:0034220)|JNK cascade (GO:0007254)|membrane organization (GO:0061024)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|negative regulation of type I interferon production (GO:0032480)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of apoptotic process (GO:0043065)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of type I interferon production (GO:0032479)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|stress-activated MAPK cascade (GO:0051403)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|transmembrane transport (GO:0055085)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral protein processing (GO:0019082)|virion assembly (GO:0019068)	cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	16				UCEC - Uterine corpus endometrioid carcinoma (92;0.0822)		AGACCATCACCCTGGAAGTGG	0.552																																					p.T90T	Melanoma(163;1126 3406 34901)	Atlas-SNP	.											UBB,bladder,carcinoma,0,2	UBB	30	2	0			c.C270T						scavenged	.						75.0	76.0	75.0					17																	16285491		2203	4297	6500	SO:0001819	synonymous_variant	7314	exon2			CATCACCCTGGAA		CCDS11177.1	17p12-p11.2	2010-11-25			ENSG00000170315	ENSG00000170315			12463	protein-coding gene	gene with protein product	"""polyubiquitin B"""	191339				2154095	Standard	NM_018955		Approved	MGC8385, FLJ25987	uc002gpx.3	P0CG47	OTTHUMG00000058987	ENST00000395837.1:c.270C>T	17.37:g.16285491C>T		Somatic	193	1	0.00518135		WXS	Illumina HiSeq	Phase_I	194	3	0.0154639	NM_018955	P02248|P02249|P02250|P62988|Q29120|Q6LBL4|Q6LDU5|Q8WYN8|Q91887|Q91888|Q9BWD6|Q9BX98|Q9UEF2|Q9UEG1|Q9UEK8|Q9UPK7	Silent	SNP	ENST00000395837.1	37	CCDS11177.1																																																																																			C|0.996;T|0.004	0.004	strong		0.552	UBB-002	NOVEL	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000130459.1	NM_018955	
HELZ2	85441	hgsc.bcm.edu	37	20	62193445	62193445	+	Missense_Mutation	SNP	G	G	A	rs3810481	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr20:62193445G>A	ENST00000467148.1	-	10	6578	c.6509C>T	c.(6508-6510)aCg>aTg	p.T2170M	HELZ2_ENST00000427522.2_Missense_Mutation_p.T1601M	NM_001037335.2	NP_001032412.2	Q9BYK8	HELZ2_HUMAN	helicase with zinc finger 2, transcriptional coactivator	2170	Interaction with THRAP3.		T -> M (in dbSNP:rs3810481).		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)										CTGAATGACCGTGAAAGGCTT	0.647													G|||	1038	0.207268	0.0068	0.085	5008	,	,		10051	0.5734		0.16	False		,,,				2504	0.2362				p.T2170M		Atlas-SNP	.											.	.	.	.	0			c.C6509T						PASS	.	G	MET/THR,MET/THR	159,4219		2,155,2032	16.0	19.0	18.0		6509,4802	4.1	0.1	20	dbSNP_107	18	1254,7310		82,1090,3110	yes	missense,missense	PRIC285	NM_001037335.2,NM_033405.3	81,81	84,1245,5142	AA,AG,GG		14.6427,3.6318,10.9179	probably-damaging,probably-damaging	2170/2650,1601/2081	62193445	1413,11529	2189	4282	6471	SO:0001583	missense	85441	exon11			ATGACCGTGAAAG	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.6509C>T	20.37:g.62193445G>A	ENSP00000417401:p.Thr2170Met	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	106	6	0.0566038	NM_001037335	Q3C2G2|Q4VXQ1|Q8TEF3|Q96ND3|Q9C094	Missense_Mutation	SNP	ENST00000467148.1	37	CCDS33508.1	504	0.23076923076923078	6	0.012195121951219513	38	0.10497237569060773	336	0.5874125874125874	124	0.16358839050131926	G	14.03	2.414176	0.42817	0.036318	0.146427	ENSG00000130589	ENST00000427522;ENST00000467148	D;D	0.84589	-1.87;-1.87	4.06	4.06	0.47325	ATPase, AAA+ type, core (1);	0.191368	0.44483	D	0.000456	T	0.00012	0.0000	M	0.87328	2.875	0.21697	P	0.999589272	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	T	0.37957	-0.9683	9	0.72032	D	0.01	-10.5405	11.8752	0.52544	0.0894:0.0:0.9106:0.0	rs3810481;rs60423961;rs3810481	2170;1601	Q9BYK8;Q9BYK8-2	PR285_HUMAN;.	M	1601;2170	ENSP00000393257:T1601M;ENSP00000417401:T2170M	ENSP00000393257:T1601M	T	-	2	0	RP4-697K14.7	61663889	1.000000	0.71417	0.078000	0.20375	0.007000	0.05969	5.234000	0.65343	1.830000	0.53286	0.313000	0.20887	ACG	G|0.836;A|0.164	0.164	strong		0.647	HELZ2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354127.1	NM_001037335	
SFT2D1	113402	hgsc.bcm.edu	37	6	166739646	166739646	+	Missense_Mutation	SNP	T	T	C	rs11551053	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr6:166739646T>C	ENST00000361731.3	-	5	434	c.325A>G	c.(325-327)Ata>Gta	p.I109V	SFT2D1_ENST00000487841.1_5'UTR	NM_145169.1	NP_660152.1			SFT2 domain containing 1									p.I109V(1)		NS(1)|central_nervous_system(1)|large_intestine(3)|upper_aerodigestive_tract(1)	6		Breast(66;0.000148)|Prostate(117;0.109)|Ovarian(120;0.199)		OV - Ovarian serous cystadenocarcinoma(33;2.63e-19)|BRCA - Breast invasive adenocarcinoma(81;4.92e-06)|GBM - Glioblastoma multiforme(31;4.58e-05)		AGGGTAAATATGAAACACAAC	0.413													C|||	557	0.111222	0.0356	0.0793	5008	,	,		18011	0.3313		0.0398	False		,,,				2504	0.0828				p.I109V		Atlas-SNP	.											SFT2D1,colon,carcinoma,+1,2	SFT2D1	12	2	1	Substitution - Missense(1)	central_nervous_system(1)	c.A325G						scavenged	.	C	VAL/ILE	147,4259	812.6+/-416.1	1,145,2057	82.0	78.0	79.0		325	-1.3	0.0	6	dbSNP_120	79	304,8296	805.6+/-407.3	5,294,4001	yes	missense	SFT2D1	NM_145169.1	29	6,439,6058	CC,CT,TT		3.5349,3.3364,3.4676	benign	109/160	166739646	451,12555	2203	4300	6503	SO:0001583	missense	113402	exon5			TAAATATGAAACA	AF041429	CCDS5292.1	6q27	2008-02-05	2005-07-25	2005-07-25	ENSG00000198818	ENSG00000198818			21102	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 83"""	C6orf83			Standard	NM_145169		Approved	MGC19825, pRGR1	uc003qux.3	Q8WV19	OTTHUMG00000016001	ENST00000361731.3:c.325A>G	6.37:g.166739646T>C	ENSP00000354590:p.Ile109Val	Somatic	298	0	0		WXS	Illumina HiSeq	Phase_I	302	10	0.0331126	NM_145169		Missense_Mutation	SNP	ENST00000361731.3	37	CCDS5292.1	278	0.12728937728937728	19	0.03861788617886179	26	0.0718232044198895	199	0.3479020979020979	34	0.044854881266490766	C	0	-2.803354	0.00075	0.033364	0.035349	ENSG00000198818	ENST00000361731	T	0.58652	0.32	4.98	-1.34	0.09143	.	0.690574	0.13904	N	0.354704	T	0.07458	0.0188	N	0.03209	-0.39	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.25012	-1.0144	9	0.02654	T	1	-6.1183	5.4909	0.16774	0.1304:0.4651:0.0:0.4045	rs11551053;rs36102427;rs60635309	109	Q8WV19	SFT2A_HUMAN	V	109	ENSP00000354590:I109V	ENSP00000354590:I109V	I	-	1	0	SFT2D1	166659636	0.000000	0.05858	0.001000	0.08648	0.007000	0.05969	-1.557000	0.02166	-0.259000	0.09432	-1.008000	0.02478	ATA	T|0.932;C|0.068	0.068	strong		0.413	SFT2D1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043061.2	NM_145169	
ABI3BP	25890	hgsc.bcm.edu	37	3	100617680	100617680	+	Silent	SNP	C	C	T	rs2245370	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr3:100617680C>T	ENST00000284322.5	-	4	517	c.408G>A	c.(406-408)tcG>tcA	p.S136S	ABI3BP_ENST00000471714.1_Silent_p.S136S|ABI3BP_ENST00000532144.1_Intron|ABI3BP_ENST00000495063.1_Silent_p.S136S	NM_015429.3	NP_056244.2	Q7Z7G0	TARSH_HUMAN	ABI family, member 3 (NESH) binding protein	136	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)	extracellular space (GO:0005615)|interstitial matrix (GO:0005614)	heparin binding (GO:0008201)			central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(18)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	50						ACAGGAAGACCGAGCTCGGTG	0.473													C|||	3646	0.728035	0.7519	0.6715	5008	,	,		19837	0.9335		0.5239	False		,,,				2504	0.7342				p.S136S		Atlas-SNP	.											.	ABI3BP	305	.	0			c.G408A						PASS	.	C		2988,1252		1079,830,211	96.0	106.0	103.0		408	-10.9	0.4	3	dbSNP_100	103	4166,4334		1012,2142,1096	no	coding-synonymous	ABI3BP	NM_015429.3		2091,2972,1307	TT,TC,CC		49.0118,29.5283,43.8462		136/1076	100617680	7154,5586	2120	4250	6370	SO:0001819	synonymous_variant	25890	exon4			GAAGACCGAGCTC	AB056106	CCDS46880.1	3q12.2	2013-02-11	2008-09-12		ENSG00000154175	ENSG00000154175		"""Fibronectin type III domain containing"""	17265	protein-coding gene	gene with protein product	"""target of Nesh-SH3"""	606279				11501947	Standard	NM_015429		Approved	NESHBP, DKFZP586L2024, TARSH	uc003dun.3	Q7Z7G0	OTTHUMG00000159094	ENST00000284322.5:c.408G>A	3.37:g.100617680C>T		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	98	6	0.0612245	NM_015429	B3KSL4|Q6ZW20|Q6ZW22|Q9C082|Q9UFI6	Silent	SNP	ENST00000284322.5	37	CCDS46880.1																																																																																			C|0.280;T|0.720	0.720	strong		0.473	ABI3BP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000353260.1		
TUBA3D	113457	hgsc.bcm.edu	37	2	132237927	132237927	+	Missense_Mutation	SNP	C	C	A	rs200147665	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr2:132237927C>A	ENST00000321253.6	+	4	768	c.661C>A	c.(661-663)Cgt>Agt	p.R221S		NM_080386.3	NP_525125.2	Q13748	TBA3C_HUMAN	tubulin, alpha 3d	221					'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|microtubule-based process (GO:0007017)|protein folding (GO:0006457)|protein polymerization (GO:0051258)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)	p.R221S(1)		breast(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(18)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)	32				BRCA - Breast invasive adenocarcinoma(221;0.13)		GGACATTGAACGTCCCACGTA	0.542																																					p.R221S	Ovarian(137;2059 2432 35543 39401)	Atlas-SNP	.											TUBA3D,trunk,malignant_melanoma,0,1	TUBA3D	60	1	1	Substitution - Missense(1)	skin(1)	c.C661A						scavenged	.						62.0	76.0	71.0					2																	132237927		2203	4296	6499	SO:0001583	missense	113457	exon4			ATTGAACGTCCCA	K03460	CCDS33290.1	2q21.1	2007-03-16			ENSG00000075886	ENSG00000075886		"""Tubulins"""	24071	protein-coding gene	gene with protein product	"""alpha-tubulin isotype H2-alpha"""					3785200	Standard	NM_080386		Approved	H2-ALPHA	uc002tsu.4	Q13748	OTTHUMG00000153600	ENST00000321253.6:c.661C>A	2.37:g.132237927C>A	ENSP00000326042:p.Arg221Ser	Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	211	4	0.0189573	NM_080386	A6NJQ0|Q5W099|Q6PEY3|Q96F18	Missense_Mutation	SNP	ENST00000321253.6	37	CCDS33290.1	.	.	.	.	.	.	.	.	.	.	c	3.464	-0.109452	0.06924	.	.	ENSG00000075886	ENST00000321253;ENST00000341158	T	0.68903	-0.36	2.24	1.33	0.21861	Tubulin/FtsZ, GTPase domain (4);	0.000000	0.44483	U	0.000448	T	0.58666	0.2138	L	0.47190	1.495	0.44036	D	0.996764	B	0.17465	0.022	B	0.32805	0.153	T	0.55049	-0.8201	10	0.87932	D	0	.	6.8167	0.23835	0.0:0.8406:0.0:0.1594	.	221	Q13748	TBA3C_HUMAN	S	221	ENSP00000326042:R221S	ENSP00000326042:R221S	R	+	1	0	TUBA3D	131954397	1.000000	0.71417	0.987000	0.45799	0.044000	0.14063	2.392000	0.44433	0.267000	0.21916	0.194000	0.17425	CGT	C|0.500;A|0.500	0.500	weak		0.542	TUBA3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331800.2	NM_080386	
KIR2DL3	3804	hgsc.bcm.edu	37	19	55263898	55263898	+	Missense_Mutation	SNP	G	G	A	rs1049267	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr19:55263898G>A	ENST00000342376.3	+	8	984	c.953G>A	c.(952-954)cGc>cAc	p.R318H	KIR2DL4_ENST00000396284.2_Intron|KIR3DL1_ENST00000541392.1_Intron|KIR3DL1_ENST00000402254.2_Intron|KIR2DL3_ENST00000434419.2_Intron|KIR3DL1_ENST00000538269.1_Intron|CTB-61M7.1_ENST00000400864.3_RNA	NM_015868.2	NP_056952.2	P43628	KI2L3_HUMAN	killer cell immunoglobulin-like receptor, two domains, long cytoplasmic tail, 3	318			R -> H (in dbSNP:rs1049267). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:8662091, ECO:0000269|PubMed:9059894, ECO:0000269|PubMed:9430221}.		immune response (GO:0006955)|regulation of immune response (GO:0050776)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	antigen binding (GO:0003823)|receptor activity (GO:0004872)			breast(1)|cervix(1)|large_intestine(1)|lung(11)|ovary(3)|pancreas(1)|skin(2)|urinary_tract(1)	21				GBM - Glioblastoma multiforme(193;0.0192)		AAAATCACTCGCCCTTCTCAG	0.498													.|||	1314	0.26238	0.2958	0.2133	5008	,	,		14495	0.1319		0.4135	False		,,,				2504	0.2311				p.R318H		Atlas-SNP	.											KIR2DL3,NS,carcinoma,0,2	KIR2DL3	68	2	0			c.G953A						scavenged	.	G	HIS/ARG	1268,2832		409,450,1191	172.0	190.0	184.0		953	-1.8	0.0	19	dbSNP_86	184	3466,4526		1194,1078,1724	no	missense	KIR2DL3	NM_015868.2	29	1603,1528,2915	AA,AG,GG		43.3684,30.9268,39.1499		318/342	55263898	4734,7358	2050	3996	6046	SO:0001583	missense	3804	exon8			TCACTCGCCCTTC	L41268	CCDS33107.1	19q13.4	2013-01-29				ENSG00000243772		"""Killer cell immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6331	protein-coding gene	gene with protein product		604938				7749980, 8662091	Standard	XM_006725426		Approved	cl-6, nkat2, nkat2a, nkat2b, p58, CD158B2		P43628	OTTHUMG00000065887	ENST00000342376.3:c.953G>A	19.37:g.55263898G>A	ENSP00000342215:p.Arg318His	Somatic	97	1	0.0103093		WXS	Illumina HiSeq	Phase_I	103	6	0.0582524	NM_015868	O43472|P78402|Q14944|Q14945|Q9UM51|Q9UQ70	Missense_Mutation	SNP	ENST00000342376.3	37	CCDS33107.1	621	0.28434065934065933	137	0.2784552845528455	96	0.26519337016574585	69	0.12062937062937062	319	0.420844327176781	g	4.003	-0.002093	0.07819	0.309268	0.433684	ENSG00000243772	ENST00000342376	T	0.00464	7.24	0.909	-1.82	0.07857	.	.	.	.	.	T	0.00012	0.0000	M	0.80028	2.48	0.80722	P	0.0	D;B;B	0.53151	0.958;0.006;0.006	P;B;B	0.48488	0.579;0.002;0.002	T	0.34428	-0.9829	8	0.42905	T	0.14	.	8.3911	0.32528	0.0:0.6188:0.3812:0.0	rs1049267;rs3189371;rs11671789;rs16985912;rs17845997;rs17858981;rs17859525	220;318;318	P43628-2;P43628;E3NZD8	.;KI2L3_HUMAN;.	H	318	ENSP00000342215:R318H	ENSP00000342215:R318H	R	+	2	0	KIR2DL3	59955710	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.002000	0.12924	-2.805000	0.00350	-2.747000	0.00125	CGC	.	.	weak		0.498	KIR2DL3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000141150.1		
RBBP8NL	140893	hgsc.bcm.edu	37	20	60989365	60989365	+	Missense_Mutation	SNP	C	C	T	rs3810553	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr20:60989365C>T	ENST00000252998.1	-	10	1198	c.1042G>A	c.(1042-1044)Gac>Aac	p.D348N		NM_080833.2	NP_543023.2	Q8NC74	RB8NL_HUMAN	RBBP8 N-terminal like	348			D -> N (in dbSNP:rs3810553). {ECO:0000269|PubMed:15489334}.			extracellular space (GO:0005615)											AGGCGAAGGTCCTGCATGCCC	0.711													C|||	1395	0.278554	0.1006	0.3487	5008	,	,		12631	0.4266		0.3211	False		,,,				2504	0.273				p.D348N		Atlas-SNP	.											.	.	.	.	0			c.G1042A						PASS	.	C	ASN/ASP	468,3542		31,406,1568	5.0	5.0	5.0		1042	0.9	0.1	20	dbSNP_107	5	1966,5974		282,1402,2286	yes	missense	C20orf151	NM_080833.2	23	313,1808,3854	TT,TC,CC		24.7607,11.6708,20.3682	benign	348/665	60989365	2434,9516	2005	3970	5975	SO:0001583	missense	140893	exon10			GAAGGTCCTGCAT	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.1042G>A	20.37:g.60989365C>T	ENSP00000252998:p.Asp348Asn	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	52	6	0.115385	NM_080833	B2RP98|Q8N4Z9|Q9BR75|Q9H0Y9	Missense_Mutation	SNP	ENST00000252998.1	37	CCDS13498.1	698	0.31959706959706957	68	0.13821138211382114	110	0.30386740331491713	264	0.46153846153846156	256	0.33773087071240104	C	12.04	1.817865	0.32145	0.116708	0.247607	ENSG00000130701	ENST00000252998	T	0.48201	0.82	5.05	0.895	0.19247	.	0.389162	0.26183	N	0.025844	T	0.00012	0.0000	L	0.46157	1.445	0.39568	P	0.030768000000000018	B	0.30033	0.266	B	0.31290	0.127	T	0.45731	-0.9241	9	0.35671	T	0.21	-13.9181	5.4657	0.16642	0.0:0.6147:0.144:0.2414	rs3810553;rs17846035;rs17859021;rs3810553	348	Q8NC74	CT151_HUMAN	N	348	ENSP00000252998:D348N	ENSP00000252998:D348N	D	-	1	0	C20orf151	60422760	0.075000	0.21258	0.123000	0.21794	0.227000	0.25037	0.339000	0.19875	-0.059000	0.13154	0.491000	0.48974	GAC	C|0.684;T|0.316	0.316	strong		0.711	RBBP8NL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080029.1	NM_080833	
TTN	7273	hgsc.bcm.edu	37	2	179444939	179444939	+	Missense_Mutation	SNP	C	C	T	rs2303838	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr2:179444939C>T	ENST00000591111.1	-	268	62376	c.62152G>A	c.(62152-62154)Gtc>Atc	p.V20718I	TTN-AS1_ENST00000456053.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.V13294I|TTN-AS1_ENST00000419746.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.V22359I|RP11-171I2.2_ENST00000603521.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.V19791I|RP11-171I2.5_ENST00000604215.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.V13419I|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.V13486I|TTN-AS1_ENST00000590807.1_RNA			Q8WZ42	TITIN_HUMAN	titin	20718	Fibronectin type-III 50. {ECO:0000255|PROSITE-ProRule:PRU00316}.		V -> I. {ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:7569978}.		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)			GTCACATTGACAGGTGGCCCA	0.348													C|||	1759	0.351238	0.3434	0.2147	5008	,	,		20260	0.631		0.1849	False		,,,				2504	0.3415				p.V22359I		Atlas-SNP	.											.	TTN	18412	.	0			c.G67075A						PASS	.	C	ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL	1207,2467		202,803,832	62.0	60.0	61.0		40456,40255,59371,39880	2.6	0.9	2	dbSNP_100	61	1445,6723		128,1189,2767	yes	missense,missense,missense,missense	TTN	NM_133437.3,NM_133432.3,NM_133378.4,NM_003319.4	29,29,29,29	330,1992,3599	TT,TC,CC		17.691,32.8525,22.3949	benign,benign,benign,benign	13486/27119,13419/27052,19791/33424,13294/26927	179444939	2652,9190	1837	4084	5921	SO:0001583	missense	7273	exon318			CATTGACAGGTGG	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.62152G>A	2.37:g.179444939C>T	ENSP00000465570:p.Val20718Ile	Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	199	9	0.0452261	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		710	0.3250915750915751	157	0.31910569105691056	73	0.20165745856353592	344	0.6013986013986014	136	0.17941952506596306	C	9.291	1.050609	0.19827	0.328525	0.17691	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.57107	0.42;0.42;0.42;0.42	5.41	2.61	0.31194	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00012	0.0000	L	0.54965	1.715	0.27033	P	0.9641858	B;B;B;B	0.10296	0.003;0.003;0.003;0.003	B;B;B;B	0.14578	0.011;0.011;0.011;0.011	T	0.39396	-0.9616	8	0.87932	D	0	.	6.7606	0.23538	0.0:0.6119:0.1229:0.2652	rs2303838;rs52803332;rs59721271;rs2303838	13294;13419;13486;20718	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	I	19791;13294;13486;13419;13292	ENSP00000343764:V19791I;ENSP00000434586:V13294I;ENSP00000340554:V13486I;ENSP00000352154:V13419I	ENSP00000340554:V13486I	V	-	1	0	TTN	179153185	0.001000	0.12720	0.932000	0.37286	0.972000	0.66771	-0.020000	0.12525	0.261000	0.21753	-0.253000	0.11424	GTC	C|0.677;T|0.323	0.323	strong		0.348	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
SEMA3E	9723	hgsc.bcm.edu	37	7	83037731	83037731	+	Missense_Mutation	SNP	C	C	G	rs61729612	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr7:83037731C>G	ENST00000307792.3	-	6	1090	c.623G>C	c.(622-624)cGa>cCa	p.R208P	SEMA3E_ENST00000427262.1_Missense_Mutation_p.R148P	NM_012431.2	NP_036563.1	O15041	SEM3E_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3E	208	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell-matrix adhesion (GO:0001953)|patterning of blood vessels (GO:0001569)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of cell shape (GO:0008360)|semaphorin-plexin signaling pathway (GO:0071526)|sprouting angiogenesis (GO:0002040)|synapse organization (GO:0050808)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)	receptor activity (GO:0004872)			breast(1)|endometrium(3)|kidney(4)|large_intestine(12)|liver(1)|lung(19)|ovary(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)	51		Medulloblastoma(109;0.109)				ATGGGCCAGTCGCCCCATGCT	0.468													C|||	489	0.0976438	0.0651	0.1081	5008	,	,		15618	0.1528		0.1243	False		,,,				2504	0.0501				p.R208P		Atlas-SNP	.											.	SEMA3E	125	.	0			c.G623C						PASS	.	C	PRO/ARG,PRO/ARG	346,4060	178.3+/-207.1	23,300,1880	68.0	63.0	64.0		443,623	1.9	0.0	7	dbSNP_129	64	1106,7494	230.5+/-264.8	89,928,3283	yes	missense,missense	SEMA3E	NM_001178129.1,NM_012431.2	103,103	112,1228,5163	GG,GC,CC		12.8605,7.8529,11.1641	benign,benign	148/716,208/776	83037731	1452,11554	2203	4300	6503	SO:0001583	missense	9723	exon6			GCCAGTCGCCCCA	AB002329	CCDS34674.1, CCDS55121.1	7q21.11	2013-01-11			ENSG00000170381	ENSG00000170381		"""Semaphorins"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10727	protein-coding gene	gene with protein product	"""M-sema H"""	608166		SEMAH		9205841, 9515811	Standard	NM_012431		Approved	M-SemaK, KIAA0331, coll-5	uc003uhy.2	O15041	OTTHUMG00000154693	ENST00000307792.3:c.623G>C	7.37:g.83037731C>G	ENSP00000303212:p.Arg208Pro	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	109	5	0.0458716	NM_012431	B4E1P1|Q75M94|Q75M97	Missense_Mutation	SNP	ENST00000307792.3	37	CCDS34674.1	259	0.11858974358974358	35	0.07113821138211382	36	0.09944751381215469	92	0.16083916083916083	96	0.1266490765171504	C	7.232	0.599571	0.13939	0.078529	0.128605	ENSG00000170381	ENST00000307792;ENST00000427262;ENST00000541514;ENST00000442159	T;T;T	0.11063	2.81;2.81;2.81	5.9	1.88	0.25563	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.528179	0.20402	N	0.093037	T	0.00039	0.0001	N	0.16201	0.385	0.80722	P	0.0	B	0.02656	0.0	B	0.13407	0.009	T	0.44605	-0.9317	9	0.13853	T	0.58	.	4.4154	0.11454	0.1454:0.5388:0.0:0.3158	rs61729612	208	O15041	SEM3E_HUMAN	P	208;148;208;148	ENSP00000303212:R208P;ENSP00000405052:R148P;ENSP00000412867:R148P	ENSP00000303212:R208P	R	-	2	0	SEMA3E	82875667	0.206000	0.23470	0.001000	0.08648	0.636000	0.38137	1.147000	0.31602	0.325000	0.23359	0.591000	0.81541	CGA	C|0.877;G|0.123	0.123	strong		0.468	SEMA3E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336606.1	NM_012431	
TMEM45A	55076	hgsc.bcm.edu	37	3	100287764	100287764	+	Silent	SNP	T	T	C	rs28722928	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr3:100287764T>C	ENST00000323523.4	+	5	1000	c.687T>C	c.(685-687)taT>taC	p.Y229Y	TMEM45A_ENST00000403410.1_Silent_p.Y245Y	NM_018004.1	NP_060474.1	Q9NWC5	TM45A_HUMAN	transmembrane protein 45A	229						integral component of membrane (GO:0016021)				breast(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|skin(2)	11						GTTGGCATTATGCAGTAACCA	0.393													T|||	1251	0.2498	0.3835	0.2493	5008	,	,		19660	0.3185		0.1213	False		,,,				2504	0.1309				p.Y229Y		Atlas-SNP	.											.	TMEM45A	35	.	0			c.T687C						PASS	.	T		1506,2900	479.4+/-358.5	266,974,963	261.0	252.0	255.0		687	-2.4	0.1	3	dbSNP_125	255	1044,7556	220.8+/-258.4	63,918,3319	no	coding-synonymous	TMEM45A	NM_018004.1		329,1892,4282	CC,CT,TT		12.1395,34.1807,19.6063		229/276	100287764	2550,10456	2203	4300	6503	SO:0001819	synonymous_variant	55076	exon5			GCATTATGCAGTA	AK000996	CCDS2937.1	3q12.2	2005-02-04			ENSG00000181458	ENSG00000181458			25480	protein-coding gene	gene with protein product						12477932	Standard	XM_005247568		Approved	FLJ10134, DERP7	uc003dtz.1	Q9NWC5	OTTHUMG00000150327	ENST00000323523.4:c.687T>C	3.37:g.100287764T>C		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	120	5	0.0416667	NM_018004	Q53YW5	Silent	SNP	ENST00000323523.4	37	CCDS2937.1																																																																																			T|0.783;C|0.217	0.217	strong		0.393	TMEM45A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317571.1	NM_018004	
FRG2B	441581	hgsc.bcm.edu	37	10	135438933	135438933	+	Silent	SNP	C	C	T	rs200793608		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr10:135438933C>T	ENST00000425520.1	-	4	559	c.507G>A	c.(505-507)ccG>ccA	p.P169P	FRG2B_ENST00000443774.1_Silent_p.P170P	NM_001080998.1	NP_001074467.1	Q96QU4	FRG2B_HUMAN	FSHD region gene 2 family, member B	169						nucleus (GO:0005634)				endometrium(2)|kidney(2)|lung(14)|ovary(1)|prostate(1)	20		all_cancers(35;7.01e-07)|all_epithelial(44;1.45e-05)|Lung NSC(174;0.027)|all_lung(145;0.0384)|all_neural(114;0.0726)|Glioma(114;0.172)|Melanoma(40;0.175)		OV - Ovarian serous cystadenocarcinoma(35;1.12e-06)|all cancers(32;1.43e-06)|Epithelial(32;1.71e-06)		TTCGAATTGACGGTGTTTGGA	0.552																																					p.P169P		Atlas-SNP	.											FRG2B,colon,carcinoma,-1,1	FRG2B	47	1	0			c.G507A						scavenged	.						126.0	151.0	143.0					10																	135438933		2193	4291	6484	SO:0001819	synonymous_variant	441581	exon4			AATTGACGGTGTT	AY744466	CCDS44502.1	10q26.3	2012-10-02			ENSG00000225899	ENSG00000225899			33518	protein-coding gene	gene with protein product						15520407	Standard	NM_001080998		Approved		uc010qvg.2	Q96QU4	OTTHUMG00000019328	ENST00000425520.1:c.507G>A	10.37:g.135438933C>T		Somatic	324	3	0.00925926		WXS	Illumina HiSeq	Phase_I	303	4	0.0132013	NM_001080998	Q5VSQ1	Silent	SNP	ENST00000425520.1	37	CCDS44502.1																																																																																			C|0.996;T|0.004	0.004	weak		0.552	FRG2B-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000467780.1	NM_001080998	
HHIPL2	79802	hgsc.bcm.edu	37	1	222713503	222713503	+	Silent	SNP	C	C	G	rs3748664	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr1:222713503C>G	ENST00000343410.6	-	4	1357	c.1299G>C	c.(1297-1299)acG>acC	p.T433T		NM_024746.3	NP_079022.2	Q6UWX4	HIPL2_HUMAN	HHIP-like 2	433					carbohydrate metabolic process (GO:0005975)	extracellular region (GO:0005576)	oxidoreductase activity, acting on the CH-OH group of donors, quinone or similar compound as acceptor (GO:0016901)|quinone binding (GO:0048038)			NS(2)|endometrium(8)|kidney(4)|large_intestine(7)|lung(28)|ovary(1)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	59				GBM - Glioblastoma multiforme(131;0.0185)		GGCCCTGGCGCGTGATGGGGT	0.567													C|||	1881	0.375599	0.3434	0.5058	5008	,	,		17111	0.5089		0.2604	False		,,,				2504	0.3078				p.T433T		Atlas-SNP	.											HHIPL2,colon,carcinoma,0,1	HHIPL2	122	1	0			c.G1299C						PASS	.	C		1446,2960	466.2+/-354.4	222,1002,979	70.0	70.0	70.0		1299	-11.0	0.0	1	dbSNP_107	70	2505,6095	408.3+/-349.4	366,1773,2161	no	coding-synonymous	HHIPL2	NM_024746.3		588,2775,3140	GG,GC,CC		29.1279,32.8189,30.3783		433/725	222713503	3951,9055	2203	4300	6503	SO:0001819	synonymous_variant	79802	exon4			CTGGCGCGTGATG	BC007638	CCDS1530.2	1q41	2008-02-05	2008-01-16	2008-01-16	ENSG00000143512	ENSG00000143512			25842	protein-coding gene	gene with protein product			"""KIAA1822-like"""	KIAA1822L		12975309	Standard	NM_024746		Approved	FLJ13840	uc001hnh.1	Q6UWX4	OTTHUMG00000037545	ENST00000343410.6:c.1299G>C	1.37:g.222713503C>G		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	60	5	0.0833333	NM_024746	Q6GU65|Q96BT4|Q96BU5|Q9H8A0	Silent	SNP	ENST00000343410.6	37	CCDS1530.2																																																																																			C|0.679;G|0.321	0.321	strong		0.567	HHIPL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091499.2	NM_024746	
CLASP2	23122	hgsc.bcm.edu	37	3	33552202	33552202	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr3:33552202C>T	ENST00000468888.2	-	37	4235	c.4189G>A	c.(4189-4191)Gag>Aag	p.E1397K	CLASP2_ENST00000307312.7_Missense_Mutation_p.E878K|CLASP2_ENST00000359576.5_Missense_Mutation_p.E1388K|CLASP2_ENST00000461133.3_Missense_Mutation_p.E1156K|CLASP2_ENST00000399362.4_Missense_Mutation_p.E1396K|CLASP2_ENST00000480013.1_Missense_Mutation_p.E1176K|CLASP2_ENST00000539981.1_3'UTR			O75122	CLAP2_HUMAN	cytoplasmic linker associated protein 2	1177					axon guidance (GO:0007411)|establishment or maintenance of cell polarity (GO:0007163)|fucosylation (GO:0036065)|microtubule anchoring (GO:0034453)|microtubule nucleation (GO:0007020)|microtubule organizing center organization (GO:0031023)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of microtubule depolymerization (GO:0007026)|regulation of microtubule polymerization or depolymerization (GO:0031110)|regulation of microtubule-based process (GO:0032886)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|kinetochore (GO:0000776)|kinetochore microtubule (GO:0005828)|membrane (GO:0016020)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|trans-Golgi network (GO:0005802)	galactoside 2-alpha-L-fucosyltransferase activity (GO:0008107)|microtubule plus-end binding (GO:0051010)			breast(2)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(19)|ovary(3)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	48						ATGCACTGCTCTGGACTAATT	0.383																																					p.E1398K		Atlas-SNP	.											.	CLASP2	138	.	0			c.G4192A						PASS	.						97.0	84.0	88.0					3																	33552202		1950	4153	6103	SO:0001583	missense	23122	exon37			ACTGCTCTGGACT	AB014527		3p24.3	2013-01-18			ENSG00000163539	ENSG00000163539			17078	protein-coding gene	gene with protein product		605853				9734811, 10899121	Standard	NM_015097		Approved	KIAA0627	uc021wvc.1	O75122	OTTHUMG00000156489	ENST00000468888.2:c.4189G>A	3.37:g.33552202C>T	ENSP00000419974:p.Glu1397Lys	Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	160	49	0.30625	NM_015097	Q7L8F6|Q8N6R6|Q9BQT3|Q9BQT4|Q9H7A3|Q9NSZ2	Missense_Mutation	SNP	ENST00000468888.2	37		.	.	.	.	.	.	.	.	.	.	C	29.9	5.044175	0.93685	.	.	ENSG00000163539	ENST00000468888;ENST00000399362;ENST00000359576;ENST00000307312;ENST00000480013;ENST00000461133	T;T;T;T;T;T	0.67345	-0.26;-0.26;-0.26;-0.26;-0.26;-0.26	6.08	6.08	0.98989	.	0.099158	0.64402	D	0.000002	T	0.72653	0.3487	M	0.71581	2.175	0.58432	D	0.999999	B;P	0.35050	0.449;0.482	B;B	0.42593	0.107;0.392	T	0.65865	-0.6064	10	0.15952	T	0.53	-20.1545	20.6634	0.99662	0.0:1.0:0.0:0.0	.	1388;1396	F5H604;E7ERI8	.;.	K	1397;1396;1388;878;1176;1156	ENSP00000419974:E1397K;ENSP00000382297:E1396K;ENSP00000352581:E1388K;ENSP00000304743:E878K;ENSP00000417518:E1176K;ENSP00000419305:E1156K	ENSP00000304743:E878K	E	-	1	0	CLASP2	33527206	1.000000	0.71417	0.997000	0.53966	0.999000	0.98932	7.506000	0.81665	2.894000	0.99253	0.655000	0.94253	GAG	.	.	none		0.383	CLASP2-001	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000344320.4	NM_001207044	
GATA3	2625	hgsc.bcm.edu	37	10	8100789	8100789	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr10:8100789G>A	ENST00000346208.3	+	3	1218	c.763G>A	c.(763-765)Gcc>Acc	p.A255T	GATA3_ENST00000379328.3_Missense_Mutation_p.A255T|GATA3_ENST00000461472.1_3'UTR			P23771	GATA3_HUMAN	GATA binding protein 3	255					anatomical structure formation involved in morphogenesis (GO:0048646)|anatomical structure morphogenesis (GO:0009653)|aortic valve morphogenesis (GO:0003180)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|canonical Wnt signaling pathway involved in metanephric kidney development (GO:0061290)|cardiac right ventricle morphogenesis (GO:0003215)|cell fate determination (GO:0001709)|cell maturation (GO:0048469)|cellular response to BMP stimulus (GO:0071773)|cellular response to interferon-alpha (GO:0035457)|cellular response to interleukin-4 (GO:0071353)|cellular response to tumor necrosis factor (GO:0071356)|defense response (GO:0006952)|developmental growth (GO:0048589)|ear development (GO:0043583)|embryonic hemopoiesis (GO:0035162)|erythrocyte differentiation (GO:0030218)|humoral immune response (GO:0006959)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|inner ear morphogenesis (GO:0042472)|interferon-gamma secretion (GO:0072643)|interleukin-4 secretion (GO:0072602)|kidney development (GO:0001822)|lens development in camera-type eye (GO:0002088)|lymphocyte migration (GO:0072676)|male gonad development (GO:0008584)|mast cell differentiation (GO:0060374)|mesenchymal to epithelial transition (GO:0060231)|mesonephros development (GO:0001823)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell motility (GO:2000146)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell proliferation involved in mesonephros development (GO:2000607)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of fibroblast growth factor receptor signaling pathway involved in ureteric bud formation (GO:2000703)|negative regulation of glial cell-derived neurotrophic factor receptor signaling pathway involved in ureteric bud formation (GO:2000734)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-2 production (GO:0032703)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|negative regulation of transcription, DNA-templated (GO:0045892)|nephric duct formation (GO:0072179)|nephric duct morphogenesis (GO:0072178)|neuron migration (GO:0001764)|norepinephrine biosynthetic process (GO:0042421)|otic vesicle development (GO:0071599)|parathyroid gland development (GO:0060017)|parathyroid hormone secretion (GO:0035898)|pharyngeal system development (GO:0060037)|phosphatidylinositol 3-kinase signaling (GO:0014065)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of interleukin-13 production (GO:0032736)|positive regulation of interleukin-13 secretion (GO:2000667)|positive regulation of interleukin-4 production (GO:0032753)|positive regulation of interleukin-5 production (GO:0032754)|positive regulation of interleukin-5 secretion (GO:2000664)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of signal transduction (GO:0009967)|positive regulation of T cell differentiation (GO:0045582)|positive regulation of thyroid hormone generation (GO:2000611)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription regulatory region DNA binding (GO:2000679)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of ureteric bud formation (GO:0072107)|post-embryonic development (GO:0009791)|pro-T cell differentiation (GO:0002572)|regulation of CD4-positive, alpha-beta T cell differentiation (GO:0043370)|regulation of cellular response to X-ray (GO:2000683)|regulation of cytokine biosynthetic process (GO:0042035)|regulation of establishment of cell polarity (GO:2000114)|regulation of histone H3-K27 methylation (GO:0061085)|regulation of histone H3-K4 methylation (GO:0051569)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of neuron apoptotic process (GO:0043523)|regulation of neuron projection development (GO:0010975)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to ethanol (GO:0045471)|response to gamma radiation (GO:0010332)|response to virus (GO:0009615)|signal transduction (GO:0007165)|sympathetic nervous system development (GO:0048485)|T cell receptor signaling pathway (GO:0050852)|T-helper 2 cell differentiation (GO:0045064)|thymic T cell selection (GO:0045061)|thymus development (GO:0048538)|TOR signaling (GO:0031929)|transcription from RNA polymerase II promoter (GO:0006366)|type IV hypersensitivity (GO:0001806)|ureter maturation (GO:0035799)|ureteric bud formation (GO:0060676)|uterus development (GO:0060065)|ventricular septum development (GO:0003281)	nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	core promoter proximal region sequence-specific DNA binding (GO:0000987)|core promoter sequence-specific DNA binding (GO:0001046)|DNA binding (GO:0003677)|E-box binding (GO:0070888)|enhancer sequence-specific DNA binding (GO:0001158)|HMG box domain binding (GO:0071837)|nucleic acid binding transcription factor activity (GO:0001071)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|transcription regulatory region sequence-specific DNA binding (GO:0000976)|zinc ion binding (GO:0008270)			NS(1)|breast(44)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(24)|ovary(3)|skin(2)	87						CAGGCCCAAGGCCCGGTCCAG	0.672			"""F, N, S"""		breast		"""HDR syndrome (HYPOPARATHYROIDISM, SENSORINEURAL DEAFNESS, AND RENAL DISEASE)"""																														p.A255T		Atlas-SNP	.		Rec	yes		10	10p15	2625	GATA binding protein 3	yes	E	.	GATA3	182	.	0			c.G763A						PASS	.						22.0	26.0	25.0					10																	8100789		2200	4297	6497	SO:0001583	missense	2625	exon3			CCCAAGGCCCGGT	X55122	CCDS7083.1, CCDS31143.1	10p15	2013-01-25	2001-11-28		ENSG00000107485	ENSG00000107485		"""GATA zinc finger domain containing"""	4172	protein-coding gene	gene with protein product		131320	"""GATA-binding protein 3"""			2050118, 15087456	Standard	NM_002051		Approved	HDR	uc001ijz.3	P23771	OTTHUMG00000017640	ENST00000346208.3:c.763G>A	10.37:g.8100789G>A	ENSP00000341619:p.Ala255Thr	Somatic	13	0	0		WXS	Illumina HiSeq	Phase_I	13	4	0.307692	NM_002051	Q5VWG7|Q5VWG8|Q96J16	Missense_Mutation	SNP	ENST00000346208.3	37	CCDS7083.1	.	.	.	.	.	.	.	.	.	.	G	9.949	1.219508	0.22373	.	.	ENSG00000107485	ENST00000379328;ENST00000346208	D;D	0.99683	-4.03;-6.39	5.55	5.55	0.83447	.	0.114990	0.64402	D	0.000016	D	0.97108	0.9055	N	0.03983	-0.305	0.42059	D	0.991155	B;B	0.12630	0.001;0.006	B;B	0.13407	0.002;0.009	D	0.97432	1.0016	10	0.10377	T	0.69	-29.272	12.7969	0.57564	0.0747:0.0:0.9253:0.0	.	255;255	P23771;P23771-2	GATA3_HUMAN;.	T	255	ENSP00000368632:A255T;ENSP00000341619:A255T	ENSP00000341619:A255T	A	+	1	0	GATA3	8140795	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	5.681000	0.68175	2.607000	0.88179	0.561000	0.74099	GCC	.	.	none		0.672	GATA3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000046719.1	NM_001002295	
PRB3	5544	hgsc.bcm.edu	37	12	11420773	11420773	+	Missense_Mutation	SNP	C	C	T	rs200940772		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr12:11420773C>T	ENST00000279573.7	-	3	545	c.410G>A	c.(409-411)cGt>cAt	p.R137H	PRB3_ENST00000381842.3_Missense_Mutation_p.R137H|PRB3_ENST00000538488.1_Intron|PRB3_ENST00000440870.3_Intron			Q04118	PRB3_HUMAN	proline-rich protein BstNI subfamily 3	137	10 X 21 AA tandem repeats of [RH]-P-G-K- P-[EQ]-G-[PQS]-P-[PS]-Q-[GE]-G-N-[QK]- [SP]-[QR]-[GR]-P-P-P.|Pro-rich.			R -> H (in Ref. 1; CAA30728). {ECO:0000305}.	defense response to Gram-negative bacterium (GO:0050829)	extracellular region (GO:0005576)				breast(2)|endometrium(1)|kidney(2)|large_intestine(1)|lung(13)|ovary(1)|skin(5)	25			OV - Ovarian serous cystadenocarcinoma(49;0.201)			CTTTCCCGGACGAGGCGGGGG	0.642																																					p.R137H		Atlas-SNP	.											PRB3,NS,carcinoma,0,2	PRB3	84	2	0			c.G410A						scavenged	.						26.0	28.0	27.0					12																	11420773		1477	3379	4856	SO:0001583	missense	5544	exon3			CCCGGACGAGGCG			12p13.2	2012-10-02				ENSG00000197870			9339	protein-coding gene	gene with protein product		168840				1894623	Standard	NM_006249		Approved	PRG	uc001qzs.3	Q04118		ENST00000279573.7:c.410G>A	12.37:g.11420773C>T	ENSP00000279573:p.Arg137His	Somatic	40	2	0.05		WXS	Illumina HiSeq	Phase_I	41	5	0.121951	NM_006249	Q15188|Q4VAY3|Q4VAY4|Q7M4M9|Q9UCT9	Missense_Mutation	SNP	ENST00000279573.7	37		.	.	.	.	.	.	.	.	.	.	.	0.011	-1.697568	0.00725	.	.	ENSG00000197870	ENST00000381842	T	0.04917	3.53	0.707	-1.41	0.08941	.	21.670500	0.01603	N	0.022149	T	0.05547	0.0146	.	.	.	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.38650	-0.9651	9	0.41790	T	0.15	.	4.061	0.09839	0.0:0.1851:0.2048:0.6101	.	137	Q04118	PRB3_HUMAN	H	137	ENSP00000371264:R137H	ENSP00000279573:R137H	R	-	2	0	PRB3	11312040	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-0.782000	0.04643	-2.300000	0.00658	-1.404000	0.01136	CGT	C|0.998;T|0.002	0.002	weak		0.642	PRB3-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000402119.5	NM_006249	
HLA-C	3107	hgsc.bcm.edu	37	6	31238009	31238009	+	Silent	SNP	T	T	C	rs1131014	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr6:31238009T>C	ENST00000376228.5	-	4	887	c.873A>G	c.(871-873)caA>caG	p.Q291Q	HLA-C_ENST00000383329.3_Silent_p.Q291Q	NM_002117.5	NP_002108.4	Q95604	1C17_HUMAN	major histocompatibility complex, class I, C	291	Alpha-3.|Ig-like C1-type.				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						TGAGGGGCTCTTGCAGCCCCT	0.592													C|||	2561	0.511382	0.6172	0.549	5008	,	,		13431	0.5744		0.4404	False		,,,				2504	0.3497				p.Q291Q		Atlas-SNP	.											HLA-C_ENST00000383329,colon,carcinoma,0,2	HLA-C	92	2	0			c.A873G						scavenged	.						23.0	30.0	28.0					6																	31238009		2121	4194	6315	SO:0001819	synonymous_variant	3107	exon4			GGGCTCTTGCAGC	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.873A>G	6.37:g.31238009T>C		Somatic	54	16	0.296296		WXS	Illumina HiSeq	Phase_I	41	18	0.439024	NM_002117	O02864|O02958|Q29643|Q9MY30	Silent	SNP	ENST00000376228.5	37	CCDS34393.1	872	0.3992673992673993	230	0.46747967479674796	148	0.4088397790055249	255	0.4458041958041958	239	0.3153034300791557	.	0.019	-1.465537	0.01053	.	.	ENSG00000204525	ENST00000415537	.	.	.	2.67	-5.33	0.02713	.	.	.	.	.	T	0.06005	0.0156	.	.	.	0.53005	P	3.799999999998249E-5	.	.	.	.	.	.	T	0.24154	-1.0168	3	.	.	.	.	2.6503	0.04996	0.1827:0.239:0.4507:0.1277	rs41551714	.	.	.	R	255	.	.	K	-	2	0	HLA-C	31345988	0.000000	0.05858	0.108000	0.21378	0.013000	0.08279	-3.876000	0.00344	-1.974000	0.00998	-0.711000	0.03637	AAG	T|0.651;C|0.349	0.349	strong		0.592	HLA-C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076281.3	NM_002117	
AQP7	364	hgsc.bcm.edu	37	9	33385235	33385235	+	3'UTR	SNP	T	T	G	rs202043723	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr9:33385235T>G	ENST00000537089.1	-	0	1197				AQP7_ENST00000377425.4_Intron			O14520	AQP7_HUMAN	aquaporin 7						excretion (GO:0007588)|generation of precursor metabolites and energy (GO:0006091)|glycerol transport (GO:0015793)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	glycerol channel activity (GO:0015254)|water channel activity (GO:0015250)	p.Y266S(3)		NS(1)|large_intestine(1)|lung(7)|ovary(1)|prostate(4)|skin(2)|stomach(1)	17			LUSC - Lung squamous cell carcinoma(29;0.00788)	GBM - Glioblastoma multiforme(74;0.191)		GCCACCTAGATAGGCACCCAG	0.592																																					p.Y266S		Atlas-SNP	.											AQP7,NS,malignant_melanoma,0,2	AQP7	58	2	3	Substitution - Missense(3)	NS(1)|lung(1)|skin(1)	c.A797C						scavenged	.						79.0	80.0	80.0					9																	33385235		2203	4300	6503	SO:0001624	3_prime_UTR_variant	364	exon8			CCTAGATAGGCAC	AB006190	CCDS6541.1	9p13	2008-02-05			ENSG00000165269	ENSG00000165269		"""Ion channels / Aquaporins"""	640	protein-coding gene	gene with protein product		602974		AQP7L		9252401	Standard	NM_001170		Approved	AQP9, AQPap	uc003zst.3	O14520	OTTHUMG00000019773	ENST00000537089.1:c.*381A>C	9.37:g.33385235T>G		Somatic	37	2	0.0540541		WXS	Illumina HiSeq	Phase_I	49	5	0.102041	NM_001170	Q08E94|Q5T5L9|Q8NHM3	Missense_Mutation	SNP	ENST00000537089.1	37		.	.	.	.	.	.	.	.	.	.	t	2.755	-0.259161	0.05791	.	.	ENSG00000165269	ENST00000379507;ENST00000297988	T;T	0.10960	2.82;2.82	4.27	0.0504	0.14293	Aquaporin-like (2);	0.887861	0.09774	N	0.757639	T	0.05960	0.0155	.	.	.	0.09310	N	0.999999	B	0.02656	0.0	B	0.04013	0.001	T	0.43393	-0.9394	9	0.26408	T	0.33	-2.9719	4.0703	0.09879	0.1654:0.202:0.0:0.6326	.	266	O14520	AQP7_HUMAN	S	265;266	ENSP00000368821:Y265S;ENSP00000297988:Y266S	ENSP00000297988:Y266S	Y	-	2	0	AQP7	33375235	0.000000	0.05858	0.589000	0.28718	0.133000	0.20885	-0.405000	0.07196	-0.060000	0.13132	-1.540000	0.00911	TAT	G|0.184;T|0.816	0.184	strong		0.592	AQP7-202	KNOWN	basic	protein_coding	protein_coding		NM_001170	
TPTE2	93492	hgsc.bcm.edu	37	13	20067011	20067011	+	Missense_Mutation	SNP	A	A	C	rs76437836	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr13:20067011A>C	ENST00000400230.2	-	3	142	c.98T>G	c.(97-99)cTg>cGg	p.L33R	TPTE2_ENST00000382978.1_Missense_Mutation_p.L33R|TPTE2_ENST00000382975.4_Missense_Mutation_p.L33R|TPTE2_ENST00000255310.6_Missense_Mutation_p.L33R|TPTE2_ENST00000382977.4_Missense_Mutation_p.L33R|TPTE2_ENST00000457266.2_Missense_Mutation_p.L33R|TPTE2_ENST00000400103.2_Missense_Mutation_p.L33R|TPTE2_ENST00000390680.2_Missense_Mutation_p.L33R			Q6XPS3	TPTE2_HUMAN	transmembrane phosphoinositide 3-phosphatase and tensin homolog 2	33					phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	ion channel activity (GO:0005216)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.L33R(1)		NS(2)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(8)|lung(21)|pancreas(1)|prostate(8)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	65		all_cancers(29;1.23e-20)|all_lung(29;1.97e-20)|all_epithelial(30;5.86e-20)|Lung NSC(5;3.36e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;1.73e-05)|Epithelial(112;7.42e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000785)|Lung(94;0.0176)|LUSC - Lung squamous cell carcinoma(192;0.089)		AGGTGACACCAGGGCTGCTCC	0.373																																					p.L33R		Atlas-SNP	.											TPTE2_ENST00000400230,adrenal_gland,adrenal_cortical_adenoma,0,3	TPTE2	225	3	1	Substitution - Missense(1)	pancreas(1)	c.T98G						scavenged	.						135.0	115.0	122.0					13																	20067011		2203	4300	6503	SO:0001583	missense	93492	exon4			GACACCAGGGCTG	AJ421032	CCDS9285.1, CCDS45013.1, CCDS45014.1	13q12.11	2012-12-10			ENSG00000132958	ENSG00000132958		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"""	17299	protein-coding gene	gene with protein product		606791				11716755, 12717346, 15057823	Standard	NM_130785		Approved	TPIP	uc001umd.3	Q6XPS3	OTTHUMG00000016493	ENST00000400230.2:c.98T>G	13.37:g.20067011A>C	ENSP00000383089:p.Leu33Arg	Somatic	152	1	0.00657895		WXS	Illumina HiSeq	Phase_I	153	7	0.0457516	NM_199254	A1A4X0|A1A4X1|A8MX64|B1AQ16|B4DWZ2|Q5VUH2|Q8WWL4|Q8WWL5	Missense_Mutation	SNP	ENST00000400230.2	37	CCDS45014.1	.	.	.	.	.	.	.	.	.	.	a	0.031	-1.334344	0.01287	.	.	ENSG00000132958	ENST00000382978;ENST00000400103;ENST00000400230;ENST00000255310;ENST00000390680;ENST00000382977;ENST00000382975;ENST00000457266;ENST00000343548;ENST00000419256	D;D;D;D;D;D;D;D	0.95171	-3.53;-3.51;-3.43;-3.63;-3.63;-3.43;-3.53;-3.51	0.785	-1.57	0.08506	.	0.817016	0.10002	N	0.728341	D	0.84629	0.5514	N	0.16478	0.41	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.0;0.001;0.0	T	0.68591	-0.5368	9	.	.	.	5.8346	1.8764	0.03219	0.3863:0.3084:0.0:0.3053	.	33;33;33	A8MX64;Q6XPS3-3;Q6XPS3	.;.;TPTE2_HUMAN	R	33	ENSP00000372438:L33R;ENSP00000382974:L33R;ENSP00000383089:L33R;ENSP00000255310:L33R;ENSP00000375098:L33R;ENSP00000372437:L33R;ENSP00000372435:L33R;ENSP00000442218:L33R	.	L	-	2	0	TPTE2	18965011	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.053000	0.01400	-1.334000	0.02244	-2.170000	0.00323	CTG	A|0.375;C|0.625	0.625	strong		0.373	TPTE2-205	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_199254	
OTOA	146183	hgsc.bcm.edu	37	16	21742188	21742188	+	Silent	SNP	G	G	A	rs76494517	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr16:21742188G>A	ENST00000286149.4	+	20	2281	c.2280G>A	c.(2278-2280)acG>acA	p.T760T	OTOA_ENST00000388958.3_Silent_p.T746T|OTOA_ENST00000388957.3_Silent_p.T422T|OTOA_ENST00000388956.4_Silent_p.T667T			Q7RTW8	OTOAN_HUMAN	otoancorin	760					cell-matrix adhesion (GO:0007160)|sensory perception of sound (GO:0007605)|transmission of nerve impulse (GO:0019226)	anchored component of membrane (GO:0031225)|apical plasma membrane (GO:0016324)|proteinaceous extracellular matrix (GO:0005578)				breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(9)|liver(2)|lung(23)|ovary(1)|prostate(1)|skin(5)|stomach(1)	46				GBM - Glioblastoma multiforme(48;0.0414)		CCGAGACCACGAAGGACTTGG	0.448																																					p.T746T		Atlas-SNP	.											OTOA_ENST00000388957,NS,haematopoietic_neoplasm,+1,3	OTOA	144	3	0			c.G2238A						scavenged	.	G	,,	17,4373	21.2+/-45.6	1,15,2179	90.0	72.0	78.0		2001,2238,1266	-8.2	0.0	16	dbSNP_131	78	25,8523	16.6+/-54.9	2,21,4251	no	coding-synonymous,coding-synonymous,coding-synonymous	OTOA	NM_001161683.1,NM_144672.3,NM_170664.2	,,	3,36,6430	AA,AG,GG		0.2925,0.3872,0.3246	,,	667/1061,746/1140,422/816	21742188	42,12896	2195	4274	6469	SO:0001819	synonymous_variant	146183	exon20			GACCACGAAGGAC	AK057335	CCDS10600.2, CCDS32403.1, CCDS53994.1	16p12.2	2009-08-18	2002-07-05		ENSG00000155719	ENSG00000155719			16378	protein-coding gene	gene with protein product	"""cancer/testis antigen 108"""	607038	"""deafness, autosomal recessive 22"""	DFNB22		11972037, 19088187	Standard	NM_170664		Approved	CT108	uc002djh.3	Q7RTW8	OTTHUMG00000090721	ENST00000286149.4:c.2280G>A	16.37:g.21742188G>A		Somatic	914	4	0.00437637		WXS	Illumina HiSeq	Phase_I	1039	20	0.0192493	NM_144672	A1L3A8|A2VDI0|B3KWU3|E9PF51|Q8NA86|Q96M76	Silent	SNP	ENST00000286149.4	37																																																																																				G|0.972;A|0.028	0.028	strong		0.448	OTOA-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000430021.1		
CCDC30	728621	hgsc.bcm.edu	37	1	43047057	43047057	+	Silent	SNP	A	A	G	rs12037518	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr1:43047057A>G	ENST00000340612.4	+	7	1092	c.1092A>G	c.(1090-1092)gaA>gaG	p.E364E	CCDC30_ENST00000390640.4_Silent_p.E153E|CCDC30_ENST00000428554.2_Silent_p.E364E|CCDC30_ENST00000507855.1_Silent_p.E153E|CCDC30_ENST00000342022.4_Silent_p.E364E			Q5VVM6	CCD30_HUMAN	coiled-coil domain containing 30	364						extracellular vesicular exosome (GO:0070062)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(11)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(2)	30						GGAAATTAGAACATGCTCATA	0.348													A|||	1397	0.278954	0.1702	0.1499	5008	,	,		18052	0.4395		0.1879	False		,,,				2504	0.4458				p.E364E		Atlas-SNP	.											.	CCDC30	78	.	0			c.A1092G						PASS	.	A		792,3614	317.7+/-295.3	72,648,1483	89.0	93.0	92.0		1092	2.0	0.8	1	dbSNP_120	92	1708,6892	311.8+/-310.5	177,1354,2769	no	coding-synonymous	CCDC30	NM_001080850.2		249,2002,4252	GG,GA,AA		19.8605,17.9755,19.2219		364/784	43047057	2500,10506	2203	4300	6503	SO:0001819	synonymous_variant	728621	exon8			ATTAGAACATGCT	AY639646	CCDS30690.1	1p34.2	2009-07-09			ENSG00000186409	ENSG00000186409			26103	protein-coding gene	gene with protein product	"""prefoldin 6-like"""					16710767	Standard	NM_001080850		Approved	FLJ20972, PFD6L, LOC728621	uc009vwk.1	Q5VVM6	OTTHUMG00000007334	ENST00000340612.4:c.1092A>G	1.37:g.43047057A>G		Somatic	381	0	0		WXS	Illumina HiSeq	Phase_I	395	17	0.043038	NM_001080850	Q14F06|Q5VVM5	Silent	SNP	ENST00000340612.4	37	CCDS30690.1																																																																																			A|0.811;G|0.189	0.189	strong		0.348	CCDC30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019524.3	NM_025030	
NOX4	50507	hgsc.bcm.edu	37	11	89088168	89088168	+	Silent	SNP	G	G	A	rs75735530	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr11:89088168G>A	ENST00000263317.4	-	13	1417	c.1179C>T	c.(1177-1179)tcC>tcT	p.S393S	NOX4_ENST00000535633.1_Silent_p.S369S|NOX4_ENST00000542487.1_Silent_p.S369S|NOX4_ENST00000343727.5_Silent_p.S369S|NOX4_ENST00000531342.1_Silent_p.S86S|NOX4_ENST00000527626.1_Silent_p.S227S|NOX4_ENST00000532825.1_Silent_p.S369S|NOX4_ENST00000413594.2_Silent_p.S414S|NOX4_ENST00000375979.3_Silent_p.S86S|NOX4_ENST00000525196.1_Intron|NOX4_ENST00000527956.1_Silent_p.S369S|NOX4_ENST00000534731.1_Silent_p.S393S|NOX4_ENST00000424319.1_Silent_p.S369S|NOX4_ENST00000528341.1_Silent_p.S368S			Q9NPH5	NOX4_HUMAN	NADPH oxidase 4	393	FAD-binding FR-type. {ECO:0000255|PROSITE-ProRule:PRU00716}.|Mediates interaction with TLR4.				bone resorption (GO:0045453)|cardiac muscle cell differentiation (GO:0055007)|cell aging (GO:0007569)|cell morphogenesis (GO:0000902)|cellular response to cAMP (GO:0071320)|cellular response to gamma radiation (GO:0071480)|cellular response to glucose stimulus (GO:0071333)|cellular response to transforming growth factor beta stimulus (GO:0071560)|homocysteine metabolic process (GO:0050667)|inflammatory response (GO:0006954)|negative regulation of cell proliferation (GO:0008285)|oxidation-reduction process (GO:0055114)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of smooth muscle cell migration (GO:0014911)|positive regulation of stress fiber assembly (GO:0051496)|reactive oxygen species metabolic process (GO:0072593)|response to hypoxia (GO:0001666)|superoxide anion generation (GO:0042554)	apical plasma membrane (GO:0016324)|endoplasmic reticulum (GO:0005783)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|NADPH oxidase complex (GO:0043020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|heme binding (GO:0020037)|modified amino acid binding (GO:0072341)|NAD(P)H oxidase activity (GO:0016174)|nucleotide binding (GO:0000166)|oxygen sensor activity (GO:0019826)|superoxide-generating NADPH oxidase activity (GO:0016175)			NS(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(8)|lung(20)|ovary(2)|prostate(3)|skin(2)	44		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.011)				GCAGAATTTCGGAGTCTTGAC	0.373													G|||	433	0.0864617	0.0023	0.1686	5008	,	,		15054	0.0883		0.0815	False		,,,				2504	0.1452				p.S393S		Atlas-SNP	.											NOX4,right_upper_lobe,carcinoma,-1,1	NOX4	101	1	0			c.C1179T						scavenged	.	G	,,	70,4332	61.1+/-98.1	1,68,2132	52.0	52.0	52.0		1179,1107,1179	-4.4	1.0	11	dbSNP_131	52	637,7953	159.7+/-212.9	25,587,3683	no	coding-synonymous,coding-synonymous,coding-synonymous	NOX4	NM_001143836.1,NM_001143837.1,NM_016931.3	,,	26,655,5815	AA,AG,GG		7.4156,1.5902,5.4418	,,	393/539,369/555,393/579	89088168	707,12285	2201	4295	6496	SO:0001819	synonymous_variant	50507	exon13			AATTTCGGAGTCT	AF254621	CCDS8285.1, CCDS44695.1, CCDS44696.1, CCDS73361.1, CCDS73362.1	11q14.2-q21	2008-02-05			ENSG00000086991	ENSG00000086991			7891	protein-coding gene	gene with protein product		605261					Standard	NM_001143837		Approved	KOX-1, KOX	uc001pct.3	Q9NPH5	OTTHUMG00000167298	ENST00000263317.4:c.1179C>T	11.37:g.89088168G>A		Somatic	341	0	0		WXS	Illumina HiSeq	Phase_I	415	13	0.0313253	NM_001143836	A8K715|B7Z520|E7EMD7|Q5K3R4|Q5K3R5|Q5K3R6|Q5K3R8|Q7Z7G3|Q86V92	Silent	SNP	ENST00000263317.4	37	CCDS8285.1																																																																																			G|0.942;A|0.058	0.058	strong		0.373	NOX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394054.1	NM_016931	
CSGALNACT2	55454	hgsc.bcm.edu	37	10	43659338	43659338	+	Silent	SNP	C	C	T	rs78146682	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr10:43659338C>T	ENST00000374466.3	+	5	1340	c.1005C>T	c.(1003-1005)acC>acT	p.T335T		NM_018590.3	NP_061060.3	Q8N6G5	CGAT2_HUMAN	chondroitin sulfate N-acetylgalactosaminyltransferase 2	335					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|chondroitin sulfate proteoglycan biosynthetic process (GO:0050650)|chondroitin sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process (GO:0050653)|dermatan sulfate proteoglycan biosynthetic process (GO:0050651)|dermatan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process (GO:0050652)|glycosaminoglycan metabolic process (GO:0030203)|proteoglycan biosynthetic process (GO:0030166)|small molecule metabolic process (GO:0044281)	Golgi cisterna membrane (GO:0032580)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)|membrane (GO:0016020)	acetylgalactosaminyltransferase activity (GO:0008376)|glucuronylgalactosylproteoglycan 4-beta-N-acetylgalactosaminyltransferase activity (GO:0047237)|metal ion binding (GO:0046872)	p.T335T(3)		endometrium(12)|kidney(3)|large_intestine(5)|lung(16)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	42						ACAATTACACCTTGGTCTCAT	0.403																																					p.T335T		Atlas-SNP	.											CSGALNACT2,NS,carcinoma,0,3	CSGALNACT2	67	3	3	Substitution - coding silent(3)	endometrium(3)	c.C1005T						scavenged	.						175.0	159.0	164.0					10																	43659338		2203	4300	6503	SO:0001819	synonymous_variant	55454	exon5			TTACACCTTGGTC	AF116646	CCDS7201.1	10q11.21	2013-02-19			ENSG00000169826	ENSG00000169826		"""Beta 4-glycosyltransferases"""	24292	protein-coding gene	gene with protein product	"""chondroitin beta1,4 N-acetylgalactosaminyltransferase 2"""					12446672	Standard	NM_018590		Approved	GALNACT2, MGC40204, PRO0082, GALNACT-2	uc001jan.4	Q8N6G5	OTTHUMG00000018023	ENST00000374466.3:c.1005C>T	10.37:g.43659338C>T		Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	139	2	0.0143885	NM_018590	B3KWL7|Q6MZJ5|Q6MZP6|Q8TCH4|Q9P1I6	Silent	SNP	ENST00000374466.3	37	CCDS7201.1																																																																																			C|0.996;T|0.005	0.005	strong		0.403	CSGALNACT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047693.1	NM_018590	
CPA2	1358	hgsc.bcm.edu	37	7	129916515	129916515	+	Silent	SNP	T	T	C	rs17590	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr7:129916515T>C	ENST00000222481.4	+	7	688	c.633T>C	c.(631-633)gaT>gaC	p.D211D		NM_001869.2	NP_001860.2	P48052	CBPA2_HUMAN	carboxypeptidase A2 (pancreatic)	211					protein catabolic process in the vacuole (GO:0007039)	extracellular region (GO:0005576)	carboxypeptidase activity (GO:0004180)|metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	14	Melanoma(18;0.0435)					CCATTCTGGATGCCCTGGATA	0.453													C|||	3467	0.692292	0.6551	0.67	5008	,	,		18837	0.7887		0.6511	False		,,,				2504	0.7014				p.D211D		Atlas-SNP	.											.	CPA2	36	.	0			c.T633C						PASS	.	C		2938,1468	472.4+/-356.4	965,1008,230	230.0	208.0	215.0		633	-1.0	0.0	7	dbSNP_63	215	5259,3341	498.1+/-374.7	1603,2053,644	no	coding-synonymous	CPA2	NM_001869.2		2568,3061,874	CC,CT,TT		38.8488,33.3182,36.9752		211/420	129916515	8197,4809	2203	4300	6503	SO:0001819	synonymous_variant	1358	exon7			TCTGGATGCCCTG	U19977	CCDS5817.2	7q32	2012-02-10			ENSG00000158516	ENSG00000158516	3.4.17.15		2297	protein-coding gene	gene with protein product		600688				7896805, 10860668	Standard	NM_001869		Approved		uc003vpq.3	P48052	OTTHUMG00000157019	ENST00000222481.4:c.633T>C	7.37:g.129916515T>C		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	113	5	0.0442478	NM_001869	A4D1M4|C9JIK1|Q53XS1|Q96A12|Q96QN3|Q9UCF1	Silent	SNP	ENST00000222481.4	37	CCDS5817.2																																																																																			T|0.354;C|0.646	0.646	strong		0.453	CPA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347124.2	NM_001869	
MUC20	200958	hgsc.bcm.edu	37	3	195452814	195452814	+	Missense_Mutation	SNP	C	C	T	rs199753483		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr3:195452814C>T	ENST00000447234.2	+	2	1466	c.1340C>T	c.(1339-1341)aCg>aTg	p.T447M	MUC20_ENST00000436408.1_Missense_Mutation_p.T447M|MUC20_ENST00000445522.2_Missense_Mutation_p.T412M|MUC20_ENST00000320736.6_Missense_Mutation_p.T276M	NM_001282506.1	NP_001269435.1	Q8N307	MUC20_HUMAN	mucin 20, cell surface associated	447					activation of MAPK activity (GO:0000187)|cellular protein metabolic process (GO:0044267)|hepatocyte growth factor receptor signaling pathway (GO:0048012)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein homooligomerization (GO:0051260)	basal plasma membrane (GO:0009925)|cell projection (GO:0042995)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)				NS(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(4)|skin(4)|stomach(3)|upper_aerodigestive_tract(1)	23	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)	Lung NSC(153;0.191)	Epithelial(36;1e-21)|all cancers(36;9.02e-20)|OV - Ovarian serous cystadenocarcinoma(49;1.6e-18)|Lung(62;0.000104)|LUSC - Lung squamous cell carcinoma(58;0.000128)	GBM - Glioblastoma multiforme(46;1.66e-05)		CTCATCCCCACGGAAGGGGTG	0.537																																					p.T276M		Atlas-SNP	.											MUC20,NS,carcinoma,0,2	MUC20	84	2	0			c.C827T						scavenged	.						35.0	31.0	32.0					3																	195452814		2053	4183	6236	SO:0001583	missense	200958	exon3			TCCCCACGGAAGG	AB037780	CCDS63877.1	3q29	2008-08-07	2006-03-14		ENSG00000176945	ENSG00000176945		"""Mucins"""	23282	protein-coding gene	gene with protein product		610360				14565953	Standard	NM_001282506		Approved	FLJ14408, KIAA1359	uc010hzo.3	Q8N307	OTTHUMG00000155823	ENST00000447234.2:c.1340C>T	3.37:g.195452814C>T	ENSP00000414350:p.Thr447Met	Somatic	440	29	0.0659091		WXS	Illumina HiSeq	Phase_I	415	31	0.0746988	NM_152673	Q6UX97|Q76I83|Q76I85|Q86ST8|Q8NBY6|Q96KA1|Q9P2I8	Missense_Mutation	SNP	ENST00000447234.2	37		.	.	.	.	.	.	.	.	.	.	C	14.09	2.432260	0.43122	.	.	ENSG00000176945	ENST00000447234;ENST00000320736;ENST00000436408;ENST00000445522	T;T;T;T	0.18016	2.67;2.72;2.84;2.24	4.38	3.51	0.40186	.	1.054240	0.07475	N	0.902873	T	0.29093	0.0723	L	0.34521	1.04	0.09310	N	1	D	0.89917	1.0	D	0.66196	0.942	T	0.20174	-1.0283	10	0.62326	D	0.03	0.7157	8.4723	0.32993	0.0:0.8925:0.0:0.1075	.	276	E9PH32	.	M	447;276;447;412	ENSP00000414350:T447M;ENSP00000325431:T276M;ENSP00000396774:T447M;ENSP00000405629:T412M	ENSP00000325431:T276M	T	+	2	0	MUC20	196938485	0.000000	0.05858	0.002000	0.10522	0.014000	0.08584	-0.101000	0.10973	1.198000	0.43158	0.514000	0.50259	ACG	C|0.996;T|0.005	0.005	weak		0.537	MUC20-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000341835.1	NM_152673	
GPRC6A	222545	hgsc.bcm.edu	37	6	117114025	117114025	+	Silent	SNP	G	G	A	rs6901250	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr6:117114025G>A	ENST00000310357.3	-	6	2082	c.2061C>T	c.(2059-2061)gcC>gcT	p.A687A	GPRC6A_ENST00000530250.1_Silent_p.A512A|GPRC6A_ENST00000368549.3_Silent_p.A616A	NM_148963.2	NP_683766.2	Q5T6X5	GPC6A_HUMAN	G protein-coupled receptor, class C, group 6, member A	687					calcium-mediated signaling (GO:0019722)|response to amino acid (GO:0043200)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.A687A(1)		autonomic_ganglia(1)|breast(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(8)|liver(1)|lung(24)|ovary(5)|pancreas(1)|skin(5)|stomach(3)|upper_aerodigestive_tract(3)	65		all_cancers(87;0.0314)|all_epithelial(87;0.0216)|Colorectal(196;0.234)		GBM - Glioblastoma multiforme(226;0.0265)|all cancers(137;0.0554)|OV - Ovarian serous cystadenocarcinoma(136;0.07)		CAAAGCTGAAGGCTAGCAAAA	0.418													G|||	1607	0.320887	0.1989	0.3703	5008	,	,		21337	0.5228		0.3082	False		,,,				2504	0.2556				p.A687A		Atlas-SNP	.											GPRC6A,NS,carcinoma,0,2	GPRC6A	152	2	1	Substitution - coding silent(1)	stomach(1)	c.C2061T						PASS	.	G		917,3489	351.8+/-311.4	94,729,1380	78.0	75.0	76.0	http://www.ncbi.nlm.nih.gov/pubmed?term	2061	0.6	1.0	6	dbSNP_116	76	2836,5764	446.8+/-361.4	457,1922,1921	yes	coding-synonymous	GPRC6A	NM_148963.2		551,2651,3301	AA,AG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	32.9767,20.8125,28.8559		687/927	117114025	3753,9253	2203	4300	6503	SO:0001819	synonymous_variant	222545	exon6			GCTGAAGGCTAGC	AF502962	CCDS5112.1, CCDS69184.1, CCDS69185.1	6q22.31	2014-01-30	2014-01-30		ENSG00000173612	ENSG00000173612		"""GPCR / Class C : Calcium-sensing receptors"""	18510	protein-coding gene	gene with protein product			"""G protein-coupled receptor, family C, group 6, member A"""				Standard	NM_001286354		Approved	bA86F4.3	uc003pxj.1	Q5T6X5	OTTHUMG00000015447	ENST00000310357.3:c.2061C>T	6.37:g.117114025G>A		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	89	8	0.0898876	NM_148963	Q6JK43|Q6JK44|Q8NGU8|Q8NHZ9|Q8TDT6	Silent	SNP	ENST00000310357.3	37	CCDS5112.1																																																																																			G|0.686;A|0.314	0.314	strong		0.418	GPRC6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041966.2		
GGT1	2678	hgsc.bcm.edu	37	22	25023419	25023419	+	Silent	SNP	C	C	T	rs202087650	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr22:25023419C>T	ENST00000400382.1	+	12	1796	c.1041C>T	c.(1039-1041)tcC>tcT	p.S347S	GGT1_ENST00000404532.1_Silent_p.S3S|GGT1_ENST00000466310.1_3'UTR|GGT1_ENST00000401885.1_Silent_p.S3S|GGT1_ENST00000248923.4_Silent_p.S347S|GGT1_ENST00000400380.1_Silent_p.S347S|GGT1_ENST00000404920.1_Silent_p.S3S|GGT1_ENST00000404223.1_Silent_p.S3S|GGT1_ENST00000403838.1_Silent_p.S3S|GGT1_ENST00000400383.1_Silent_p.S347S|GGT1_ENST00000406383.2_Silent_p.S347S			P19440	GGT1_HUMAN	gamma-glutamyltransferase 1	347					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)	ACATGACCTCCGAGTTCTTCG	0.647																																					p.S347S		Atlas-SNP	.											GGT1,NS,carcinoma,0,2	GGT1	68	2	0			c.C1041T						scavenged	.						53.0	54.0	54.0					22																	25023419		2201	4297	6498	SO:0001819	synonymous_variant	2678	exon12			GACCTCCGAGTTC	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.1041C>T	22.37:g.25023419C>T		Somatic	238	8	0.0336134		WXS	Illumina HiSeq	Phase_I	254	10	0.0393701	NM_013430	Q08247|Q14404|Q8TBS1|Q9UMK1	Silent	SNP	ENST00000400382.1	37	CCDS42992.1																																																																																			C|0.989;T|0.011	0.011	strong		0.647	GGT1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250797.1	NM_013430	
VWA5B1	127731	hgsc.bcm.edu	37	1	20671961	20671961	+	Missense_Mutation	SNP	G	G	A	rs11582960	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr1:20671961G>A	ENST00000375079.2	+	17	2835	c.2639G>A	c.(2638-2640)cGc>cAc	p.R880H	VWA5B1_ENST00000289815.8_Missense_Mutation_p.R880H|VWA5B1_ENST00000375083.4_Missense_Mutation_p.R880H|VWA5B1_ENST00000525343.1_3'UTR	NM_001039500.2	NP_001034589.2	Q5TIE3	VW5B1_HUMAN	von Willebrand factor A domain containing 5B1	880				R -> H (in Ref. 3; AAI01381). {ECO:0000305}.		extracellular region (GO:0005576)				central_nervous_system(1)|endometrium(3)|kidney(1)|prostate(1)|skin(1)	7						TCCAACCGCCGCTACCAAGTG	0.557													G|||	1511	0.301717	0.2443	0.3458	5008	,	,		16591	0.3532		0.3181	False		,,,				2504	0.2781				p.R880H		Atlas-SNP	.											VWA5B1,colon,carcinoma,0,1	VWA5B1	44	1	0			c.G2639A						scavenged	.	G	HIS/ARG	342,1042		37,268,387	34.0	29.0	30.0		2639	5.3	1.0	1	dbSNP_120	30	1056,2126		168,720,703	yes	missense	VWA5B1	NM_001039500.2	29	205,988,1090	AA,AG,GG		33.1867,24.711,30.6176	probably-damaging	880/1216	20671961	1398,3168	692	1591	2283	SO:0001583	missense	127731	exon17			ACCGCCGCTACCA	AK125833, AK057346		1p36.12	2014-02-12			ENSG00000158816	ENSG00000158816			26538	protein-coding gene	gene with protein product							Standard	NM_001039500		Approved	FLJ32784	uc009vps.2	Q5TIE3	OTTHUMG00000002835	ENST00000375079.2:c.2639G>A	1.37:g.20671961G>A	ENSP00000364220:p.Arg880His	Somatic	253	1	0.00395257		WXS	Illumina HiSeq	Phase_I	248	5	0.0201613	NM_001039500	A4IF35|A4IF36|Q3ZCM4|Q6ZUB4|Q96M71	Missense_Mutation	SNP	ENST00000375079.2	37		693	0.3173076923076923	101	0.20528455284552846	125	0.3453038674033149	238	0.4160839160839161	229	0.3021108179419525	G	20.2	3.952435	0.73787	0.24711	0.331867	ENSG00000158816	ENST00000375089;ENST00000289815;ENST00000375083;ENST00000375079	T;T;T	0.12774	3.01;2.65;3.01	5.28	5.28	0.74379	.	0.070917	0.56097	D	0.000025	T	0.00012	0.0000	L	0.47716	1.5	0.09310	P	0.9999999999999946	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.991;0.999;0.983	T	0.48864	-0.8997	9	0.87932	D	0	-10.357	16.3895	0.83528	0.0:0.0:1.0:0.0	rs11582960;rs52789768;rs11582960	880;880;880	Q5TIE3;Q5TIE3-5;Q5TIE3-2	VW5B1_HUMAN;.;.	H	880	ENSP00000289815:R880H;ENSP00000364224:R880H;ENSP00000364220:R880H	ENSP00000289815:R880H	R	+	2	0	VWA5B1	20544548	1.000000	0.71417	1.000000	0.80357	0.917000	0.54804	5.758000	0.68776	2.470000	0.83445	0.573000	0.79308	CGC	G|0.696;A|0.304	0.304	strong		0.557	VWA5B1-001	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000007945.4	XM_001722222	
RBM23	55147	hgsc.bcm.edu	37	14	23371055	23371055	+	Missense_Mutation	SNP	G	G	C	rs1127066	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr14:23371055G>C	ENST00000359890.3	-	13	1479	c.1284C>G	c.(1282-1284)ttC>ttG	p.F428L	RBM23_ENST00000346528.5_Missense_Mutation_p.F394L|RBM23_ENST00000542016.2_Missense_Mutation_p.F258L|RBM23_ENST00000399922.2_Missense_Mutation_p.F412L|RBM23_ENST00000555209.1_Missense_Mutation_p.F178L	NM_001077351.1	NP_001070819.1	Q86U06	RBM23_HUMAN	RNA binding motif protein 23	428			F -> L (in dbSNP:rs1127066).		mRNA processing (GO:0006397)	membrane (GO:0016020)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			endometrium(3)|kidney(2)|lung(3)|prostate(1)|skin(1)	10	all_cancers(95;4.69e-05)			GBM - Glioblastoma multiforme(265;0.0128)		TGGAGAGCTGGAAACACTGGG	0.527													G|||	1076	0.214856	0.053	0.2983	5008	,	,		19620	0.2649		0.2853	False		,,,				2504	0.2505				p.F428L		Atlas-SNP	.											.	RBM23	44	.	0			c.C1284G						PASS	.	G	LEU/PHE,LEU/PHE,LEU/PHE	381,3653		20,341,1656	166.0	176.0	173.0		1284,1182,1236	2.3	1.0	14	dbSNP_86	173	2510,5860		387,1736,2062	yes	missense,missense,missense	RBM23	NM_001077351.1,NM_001077352.1,NM_018107.4	22,22,22	407,2077,3718	CC,CG,GG		29.9881,9.4447,23.307	possibly-damaging,possibly-damaging,possibly-damaging	428/440,394/406,412/424	23371055	2891,9513	2017	4185	6202	SO:0001583	missense	55147	exon13			GAGCTGGAAACAC	AF275678	CCDS41919.1, CCDS41920.1, CCDS41921.1	14q11.1	2014-07-03	2004-04-23	2004-04-23		ENSG00000100461		"""RNA binding motif (RRM) containing"""	20155	protein-coding gene	gene with protein product	"""coactivator of activating protein-1 and estrogen recep- tors beta"""		"""RNA-binding region (RNP1, RRM) containing 4"""	RNPC4		15694343	Standard	NM_018107		Approved	FLJ10482, CAPERbeta	uc001whg.3	Q86U06		ENST00000359890.3:c.1284C>G	14.37:g.23371055G>C	ENSP00000352956:p.Phe428Leu	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	130	8	0.0615385	NM_001077351	D3DS32|Q8ND16|Q8TB88|Q8WY40|Q9BUJ1|Q9NVV7	Missense_Mutation	SNP	ENST00000359890.3	37	CCDS41921.1	509|509	0.23305860805860806|0.23305860805860806	37|37	0.07520325203252033|0.07520325203252033	107|107	0.2955801104972376|0.2955801104972376	154|154	0.2692307692307692|0.2692307692307692	211|211	0.2783641160949868|0.2783641160949868	G|G	12.07|12.07	1.826883|1.826883	0.32329|0.32329	0.094447|0.094447	0.299881|0.299881	ENSG00000100461|ENSG00000100461	ENST00000555209;ENST00000359890;ENST00000338980;ENST00000399922;ENST00000346528;ENST00000542016;ENST00000557245|ENST00000553884	T;T;T;T;T;T|.	0.47528|.	0.84;0.84;0.84;0.84;0.84;0.84|.	5.34|5.34	2.35|2.35	0.29111|0.29111	.|.	0.314942|.	0.26072|.	N|.	0.026512|.	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.35854|0.35854	1.095|1.095	0.23298|0.23298	P|P	0.9979592|0.9979592	B;B;B|.	0.23735|.	0.002;0.002;0.09|.	B;B;B|.	0.23574|.	0.019;0.019;0.047|.	T|T	0.26360|0.26360	-1.0105|-1.0105	9|4	0.15066|.	T|.	0.55|.	-0.3141|-0.3141	10.3266|10.3266	0.43796|0.43796	0.0:0.1306:0.599:0.2704|0.0:0.1306:0.599:0.2704	rs1127066;rs1242630;rs1742324;rs3182572;rs11557897;rs17124077;rs52811176;rs59971662;rs1127066|rs1127066;rs1242630;rs1742324;rs3182572;rs11557897;rs17124077;rs52811176;rs59971662;rs1127066	394;412;428|.	Q86U06-4;Q86U06-2;Q86U06|.	.;.;RBM23_HUMAN|.	L|A	178;428;405;412;394;258;71|203	ENSP00000452602:F178L;ENSP00000352956:F428L;ENSP00000382806:F412L;ENSP00000339220:F394L;ENSP00000438504:F258L;ENSP00000451838:F71L|.	ENSP00000345496:F405L|.	F|P	-|-	3|1	2|0	RBM23|RBM23	22440895|22440895	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.982000|0.982000	0.71751|0.71751	0.348000|0.348000	0.20031|0.20031	0.190000|0.190000	0.20209|0.20209	0.561000|0.561000	0.74099|0.74099	TTC|CCA	G|0.760;C|0.240	0.240	strong		0.527	RBM23-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000413545.3		
NEB	4703	hgsc.bcm.edu	37	2	152422087	152422087	+	Silent	SNP	A	A	G	rs2288211	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr2:152422087A>G	ENST00000172853.10	-	88	13338	c.13191T>C	c.(13189-13191)taT>taC	p.Y4397Y	NEB_ENST00000604864.1_Silent_p.Y6098Y|NEB_ENST00000427231.2_Silent_p.Y6098Y|NEB_ENST00000603639.1_Silent_p.Y6098Y|NEB_ENST00000409198.1_Silent_p.Y4397Y|NEB_ENST00000397345.3_Silent_p.Y6098Y			P20929	NEBU_HUMAN	nebulin	4397					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)	p.Y4397Y(1)		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)		TAAAGTTAGGATAGTTTTCAA	0.388													A|||	1121	0.223842	0.0363	0.3761	5008	,	,		19432	0.3036		0.328	False		,,,				2504	0.18				p.Y6098Y		Atlas-SNP	.											NEB,NS,carcinoma,0,1	NEB	1697	1	1	Substitution - coding silent(1)	stomach(1)	c.T18294C						PASS	.	A	,,	314,3372		8,298,1537	70.0	63.0	65.0		18294,18294,13191	1.2	1.0	2	dbSNP_100	65	2380,5802		349,1682,2060	no	coding-synonymous,coding-synonymous,coding-synonymous	NEB	NM_001164507.1,NM_001164508.1,NM_004543.4	,,	357,1980,3597	GG,GA,AA		29.0882,8.5187,22.6997	,,	6098/8526,6098/8526,4397/6670	152422087	2694,9174	1843	4091	5934	SO:0001819	synonymous_variant	4703	exon116			GTTAGGATAGTTT	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.13191T>C	2.37:g.152422087A>G		Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	179	9	0.0502793	NM_001271208	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Silent	SNP	ENST00000172853.10	37																																																																																				A|0.732;G|0.268	0.268	strong		0.388	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543	
GPR128	84873	hgsc.bcm.edu	37	3	100368546	100368546	+	Missense_Mutation	SNP	A	A	G	rs61730367	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr3:100368546A>G	ENST00000273352.3	+	11	1542	c.1274A>G	c.(1273-1275)aAa>aGa	p.K425R	GPR128_ENST00000475887.1_Missense_Mutation_p.K130R	NM_032787.2	NP_116176.2	Q96K78	GP128_HUMAN	G protein-coupled receptor 128	425	GPS. {ECO:0000255|PROSITE- ProRule:PRU00098}.				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(1)|autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(9)|liver(2)|lung(20)|ovary(3)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	56						CAGACTTTCAAAAAGGATTAT	0.353													A|||	609	0.121605	0.0802	0.1643	5008	,	,		19359	0.251		0.0497	False		,,,				2504	0.0879				p.K425R	Pancreas(87;185 1975 7223 18722)	Atlas-SNP	.											.	GPR128	126	.	0			c.A1274G						PASS	.	A	ARG/LYS	334,4070	166.9+/-198.0	10,314,1878	98.0	93.0	95.0		1274	-1.6	0.6	3	dbSNP_129	95	444,8156	127.7+/-186.0	10,424,3866	yes	missense	GPR128	NM_032787.2	26	20,738,5744	GG,GA,AA		5.1628,7.584,5.9828	benign	425/798	100368546	778,12226	2202	4300	6502	SO:0001583	missense	84873	exon11			CTTTCAAAAAGGA	AK027360	CCDS2938.1	3q12.3	2014-08-08			ENSG00000144820	ENSG00000144820		"""-"", ""GPCR / Class B : Orphans"""	19241	protein-coding gene	gene with protein product		612307					Standard	NM_032787		Approved	FLJ14454	uc003duc.3	Q96K78	OTTHUMG00000159083	ENST00000273352.3:c.1274A>G	3.37:g.100368546A>G	ENSP00000273352:p.Lys425Arg	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	100	5	0.05	NM_032787	Q14D94|Q86SQ2	Missense_Mutation	SNP	ENST00000273352.3	37	CCDS2938.1	284	0.13003663003663005	26	0.052845528455284556	63	0.17403314917127072	155	0.270979020979021	40	0.052770448548812667	A	10.44	1.351018	0.24512	0.07584	0.051628	ENSG00000144820	ENST00000273352;ENST00000475887	T;T	0.38240	1.15;1.46	5.49	-1.61	0.08399	GPS domain (2);	0.968711	0.08539	N	0.930924	T	0.00012	0.0000	N	0.21373	0.66	0.80722	P	0.0	B;B	0.06786	0.0;0.001	B;B	0.08055	0.003;0.001	T	0.38178	-0.9673	9	0.08179	T	0.78	.	5.1415	0.14961	0.5914:0.0:0.286:0.1226	rs61730367	130;425	E9PHI0;Q96K78	.;GP128_HUMAN	R	425;130	ENSP00000273352:K425R;ENSP00000419788:K130R	ENSP00000273352:K425R	K	+	2	0	GPR128	101851236	0.001000	0.12720	0.560000	0.28344	0.455000	0.32408	-0.066000	0.11598	-0.200000	0.10300	-0.327000	0.08410	AAA	A|0.920;G|0.080	0.080	strong		0.353	GPR128-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353236.1		
FAM131C	348487	hgsc.bcm.edu	37	1	16384999	16384999	+	Missense_Mutation	SNP	G	G	A	rs1807284	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr1:16384999G>A	ENST00000375662.4	-	7	959	c.776C>T	c.(775-777)cCc>cTc	p.P259L	FAM131C_ENST00000494078.1_5'UTR	NM_182623.2	NP_872429.2	Q96AQ9	F131C_HUMAN	family with sequence similarity 131, member C	259	Pro-rich.									large_intestine(2)|lung(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	8		Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Colorectal(212;8.32e-08)|COAD - Colon adenocarcinoma(227;5.56e-06)|BRCA - Breast invasive adenocarcinoma(304;9.12e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.00656)|READ - Rectum adenocarcinoma(331;0.0649)		GGAGCCCGGGGGGTGGGTCCC	0.721													A|||	1887	0.376797	0.4032	0.2795	5008	,	,		19329	0.4315		0.336	False		,,,				2504	0.3957				p.P259L		Atlas-SNP	.											FAM131C,NS,carcinoma,0,2	FAM131C	21	2	0			c.C776T						scavenged	.						2.0	3.0	3.0					1																	16384999		1408	3137	4545	SO:0001583	missense	348487	exon7			CCCGGGGGGTGGG		CCDS41270.1	1p36.13	2008-02-05	2007-03-20	2007-03-20	ENSG00000185519	ENSG00000185519			26717	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 117"""	C1orf117		12477932	Standard	NM_182623		Approved	FLJ36766	uc001axz.4	Q96AQ9	OTTHUMG00000009525	ENST00000375662.4:c.776C>T	1.37:g.16384999G>A	ENSP00000364814:p.Pro259Leu	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	132	5	0.0378788	NM_182623	Q5T5Q5|Q8N3X3|Q8N9P9	Missense_Mutation	SNP	ENST00000375662.4	37	CCDS41270.1	618	0.28296703296703296	170	0.34552845528455284	94	0.2596685082872928	168	0.2937062937062937	186	0.24538258575197888	A	0.006	-2.029401	0.00410	.	.	ENSG00000185519	ENST00000375662	T	0.11821	2.74	4.65	-2.16	0.07080	.	1.628260	0.03484	N	0.215578	T	0.00012	0.0000	N	0.00972	-1.085	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.43605	-0.9381	10	0.02654	T	1	.	10.8536	0.46784	0.4433:0.0:0.5567:0.0	rs1807284;rs3884147	259	Q96AQ9	F131C_HUMAN	L	259	ENSP00000364814:P259L	ENSP00000364814:P259L	P	-	2	0	FAM131C	16257586	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.041000	0.12084	-1.034000	0.03295	-1.271000	0.01417	CCC	G|0.717;A|0.283	0.283	strong		0.721	FAM131C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026319.1	NM_182623	
MBL2	4153	hgsc.bcm.edu	37	10	54528266	54528266	+	Silent	SNP	G	G	C	rs930507	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr10:54528266G>C	ENST00000373968.3	-	4	442	c.378C>G	c.(376-378)ctC>ctG	p.L126L		NM_000242.2	NP_000233.1	P11226	MBL2_HUMAN	mannose-binding lectin (protein C) 2, soluble	126					acute-phase response (GO:0006953)|complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|complement activation, lectin pathway (GO:0001867)|defense response to bacterium (GO:0042742)|defense response to Gram-positive bacterium (GO:0050830)|innate immune response (GO:0045087)|killing by host of symbiont cells (GO:0051873)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of viral process (GO:0048525)|opsonization (GO:0008228)|positive regulation of phagocytosis (GO:0050766)|response to oxidative stress (GO:0006979)	cell surface (GO:0009986)|collagen trimer (GO:0005581)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	calcium-dependent protein binding (GO:0048306)|mannose binding (GO:0005537)|receptor binding (GO:0005102)			breast(1)|endometrium(2)|lung(12)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	21						GAGAGAAGGTGAGCCCTAAAA	0.423													C|||	3700	0.738818	0.6399	0.8559	5008	,	,		18473	0.7302		0.8032	False		,,,				2504	0.7321				p.L126L		Atlas-SNP	.											MBL2,colon,carcinoma,0,1	MBL2	55	1	0			c.C378G	GRCh37	CM068190	MBL2	M	rs930507	scavenged	.	C		2926,1478	467.4+/-354.8	994,938,270	73.0	78.0	76.0		378	-4.6	0.0	10	dbSNP_86	76	7095,1505	281.8+/-295.3	2935,1225,140	no	coding-synonymous	MBL2	NM_000242.2		3929,2163,410	CC,CG,GG		17.5,33.5604,22.9391		126/249	54528266	10021,2983	2202	4300	6502	SO:0001819	synonymous_variant	4153	exon4			GAAGGTGAGCCCT	AF360991	CCDS7247.1	10q11.2	2014-09-17	2011-02-02		ENSG00000165471	ENSG00000165471		"""Collectins"""	6922	protein-coding gene	gene with protein product		154545	"""mannose-binding lectin (protein C) 2, soluble (opsonic defect)"""	MBL		1675710, 1672848	Standard	NM_000242		Approved	COLEC1	uc001jjt.3	P11226	OTTHUMG00000150270	ENST00000373968.3:c.378C>G	10.37:g.54528266G>C		Somatic	53	1	0.0188679		WXS	Illumina HiSeq	Phase_I	58	2	0.0344828	NM_000242	Q4VB12|Q4VB13|Q4VB14|Q5SQS3|Q86SI4|Q96KE4|Q96TF7|Q96TF8|Q96TF9	Silent	SNP	ENST00000373968.3	37	CCDS7247.1																																																																																			G|0.238;C|0.762	0.762	strong		0.423	MBL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048115.1	NM_000242	
PLD4	122618	hgsc.bcm.edu	37	14	105395204	105395204	+	Missense_Mutation	SNP	G	G	A	rs3803295	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr14:105395204G>A	ENST00000392593.4	+	4	571	c.403G>A	c.(403-405)Gtg>Atg	p.V135M	PLD4_ENST00000540372.1_Missense_Mutation_p.V142M	NM_138790.2	NP_620145.2	Q96BZ4	PLD4_HUMAN	phospholipase D family, member 4	135			V -> M (in dbSNP:rs3803295).		glycerophospholipid biosynthetic process (GO:0046474)|hematopoietic progenitor cell differentiation (GO:0002244)|inositol phosphate metabolic process (GO:0043647)|lipid catabolic process (GO:0016042)|phagocytosis (GO:0006909)|phosphatidylglycerol biosynthetic process (GO:0006655)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|phagocytic vesicle (GO:0045335)|trans-Golgi network membrane (GO:0032588)	N-acylphosphatidylethanolamine-specific phospholipase D activity (GO:0070290)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase D activity (GO:0004630)			central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(7)|ovary(1)|skin(1)|urinary_tract(1)	13		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.00067)|OV - Ovarian serous cystadenocarcinoma(23;0.00976)|Epithelial(46;0.0201)|GBM - Glioblastoma multiforme(11;0.116)			GAGCGTCCACGTGGCTTCATA	0.687													g|||	10	0.00199681	0.0	0.0	5008	,	,		18064	0.0089		0.001	False		,,,				2504	0.0				p.V135M		Atlas-SNP	.											.	PLD4	46	.	0			c.G403A						PASS	.						48.0	52.0	51.0					14																	105395204		2055	4215	6270	SO:0001583	missense	122618	exon4			GTCCACGTGGCTT		CCDS9995.2	14q32.33	2014-01-28	2005-05-20	2005-05-20	ENSG00000166428	ENSG00000166428			23792	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 175"""	C14orf175			Standard	XM_006720024		Approved		uc001ypu.1	Q96BZ4	OTTHUMG00000144167	ENST00000392593.4:c.403G>A	14.37:g.105395204G>A	ENSP00000376372:p.Val135Met	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	133	6	0.0451128	NM_138790	Q6UWD2	Missense_Mutation	SNP	ENST00000392593.4	37	CCDS9995.2	9	0.004120879120879121	0	0.0	0	0.0	9	0.015734265734265736	0	0.0	G	11.99	1.804171	0.31869	.	.	ENSG00000166428	ENST00000540372;ENST00000392593;ENST00000557573	T;T;T	0.14516	2.5;2.5;2.5	4.45	2.58	0.30949	.	0.275018	0.29198	N	0.012858	T	0.05960	0.0155	L	0.55990	1.75	0.80722	D	1	B;B	0.33212	0.402;0.281	B;B	0.32533	0.147;0.07	T	0.07233	-1.0783	10	0.49607	T	0.09	7.0948	6.3692	0.21471	0.3264:0.0:0.6736:0.0	rs3803295;rs3803295	142;135	F5H2B5;Q96BZ4	.;PLD4_HUMAN	M	142;135;133	ENSP00000438677:V142M;ENSP00000376372:V135M;ENSP00000451278:V133M	ENSP00000376372:V135M	V	+	1	0	PLD4	104466249	0.290000	0.24343	0.256000	0.24389	0.446000	0.32137	0.534000	0.23098	0.413000	0.25759	0.645000	0.84053	GTG	G|0.994;A|0.006	0.006	strong		0.687	PLD4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000291348.2	NM_138790	
CCDC102B	79839	hgsc.bcm.edu	37	18	66564514	66564514	+	Missense_Mutation	SNP	G	G	C	rs117721069	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr18:66564514G>C	ENST00000360242.5	+	6	1229	c.1112G>C	c.(1111-1113)aGa>aCa	p.R371T	CCDC102B_ENST00000577772.1_3'UTR|CCDC102B_ENST00000319445.6_Missense_Mutation_p.R371T|CCDC102B_ENST00000584156.1_Missense_Mutation_p.R371T|RP11-861L17.3_ENST00000584226.1_5'Flank|CCDC102B_ENST00000358653.5_Missense_Mutation_p.R371T	NM_024781.2	NP_079057	Q68D86	C102B_HUMAN	coiled-coil domain containing 102B	371										breast(2)|endometrium(3)|large_intestine(5)|lung(19)|ovary(1)|skin(5)|stomach(1)	36		Esophageal squamous(42;0.0559)|Colorectal(73;0.0604)				ATACTTGAAAGAGAAAAGCAG	0.408													C|||	96	0.0191693	0.0023	0.0	5008	,	,		18156	0.0665		0.0139	False		,,,				2504	0.0123				p.R371T		Atlas-SNP	.											.	CCDC102B	92	.	0			c.G1112C						PASS	.	C	THR/ARG,THR/ARG	34,4372	822.3+/-416.4	0,34,2169	112.0	121.0	118.0		1112,1112	1.6	0.2	18	dbSNP_132	118	67,8533	815.5+/-407.0	1,65,4234	yes	missense,missense	CCDC102B	NM_001093729.1,NM_024781.2	71,71	1,99,6403	CC,CG,GG		0.7791,0.7717,0.7766	benign,benign	371/514,371/514	66564514	101,12905	2203	4300	6503	SO:0001583	missense	79839	exon8			TTGAAAGAGAAAA	AK027247	CCDS11996.2	18q22.1	2007-11-14	2006-04-10	2006-04-10	ENSG00000150636	ENSG00000150636			26295	protein-coding gene	gene with protein product			"""chromosome 18 open reading frame 14"", ""aminoacylase 1-like"""	C18orf14, ACY1L		14702039	Standard	NM_001093729		Approved	FLJ23594, HsT1731, AN	uc002lkk.2	Q68D86	OTTHUMG00000132808	ENST00000360242.5:c.1112G>C	18.37:g.66564514G>C	ENSP00000353377:p.Arg371Thr	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	104	5	0.0480769	NM_001093729	Q7Z467|Q8NDK7|Q9H5C1	Missense_Mutation	SNP	ENST00000360242.5	37	CCDS11996.2	51	0.023351648351648352	1	0.0020325203252032522	0	0.0	38	0.06643356643356643	12	0.0158311345646438	C	10.75	1.439360	0.25900	0.007717	0.007791	ENSG00000150636	ENST00000319445;ENST00000358653;ENST00000360242	T;T;T	0.10005	3.43;2.92;3.43	5.43	1.62	0.23740	.	0.429480	0.22448	N	0.059924	T	0.00144	0.0004	N	0.00223	-1.815	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.38628	-0.9652	10	0.02654	T	1	-0.0786	2.2253	0.03982	0.1374:0.4998:0.1333:0.2296	.	371;371	Q68D86-3;Q68D86	.;C102B_HUMAN	T	371	ENSP00000316237:R371T;ENSP00000351479:R371T;ENSP00000353377:R371T	ENSP00000316237:R371T	R	+	2	0	CCDC102B	64715494	1.000000	0.71417	0.179000	0.23059	0.984000	0.73092	1.359000	0.34113	0.029000	0.15352	-0.216000	0.12614	AGA	G|0.988;C|0.012	0.012	strong		0.408	CCDC102B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256225.2	NM_024781	
UBC	7316	hgsc.bcm.edu	37	12	125397358	125397358	+	Silent	SNP	T	T	C			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr12:125397358T>C	ENST00000536769.1	-	1	2536	c.960A>G	c.(958-960)gaA>gaG	p.E320E	MIR5188_ENST00000583467.1_RNA|UBC_ENST00000538617.1_Intron|UBC_ENST00000339647.5_Silent_p.E320E|UBC_ENST00000546120.1_Silent_p.E244E|UBC_ENST00000536661.1_5'Flank			P0CG48	UBC_HUMAN	ubiquitin C	320	Ubiquitin-like 5. {ECO:0000255|PROSITE- ProRule:PRU00214}.				activation of MAPK activity (GO:0000187)|anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|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 peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|carbohydrate metabolic process (GO:0005975)|cellular response to hypoxia (GO:0071456)|cytokine-mediated signaling pathway (GO:0019221)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|endosomal transport (GO:0016197)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|gene expression (GO:0010467)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|innate immune response (GO:0045087)|intracellular transport of virus (GO:0075733)|ion transmembrane transport (GO:0034220)|JNK cascade (GO:0007254)|membrane organization (GO:0061024)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|negative regulation of type I interferon production (GO:0032480)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of apoptotic process (GO:0043065)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of type I interferon production (GO:0032479)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|stress-activated MAPK cascade (GO:0051403)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|transmembrane transport (GO:0055085)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral protein processing (GO:0019082)|virion assembly (GO:0019068)	cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)|protease binding (GO:0002020)	p.E320E(1)		breast(3)|endometrium(4)|kidney(4)|large_intestine(2)|lung(13)|ovary(3)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	36	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;6.17e-05)|Epithelial(86;0.000207)|all cancers(50;0.00308)		TCGGCTCCACTTCGAGAGTGA	0.522																																					p.E320E		Atlas-SNP	.											UBC,NS,carcinoma,0,2	UBC	79	2	1	Substitution - coding silent(1)	prostate(1)	c.A960G						scavenged	.						92.0	81.0	85.0					12																	125397358		2202	4282	6484	SO:0001819	synonymous_variant	7316	exon2			CTCCACTTCGAGA		CCDS9260.1	12q24.3	2008-09-08			ENSG00000150991	ENSG00000150991			12468	protein-coding gene	gene with protein product	"""polyubiquitin-C"""	191340				1315303, 11872750	Standard	NM_021009		Approved		uc001ugs.4	P0CG48		ENST00000536769.1:c.960A>G	12.37:g.125397358T>C		Somatic	246	0	0		WXS	Illumina HiSeq	Phase_I	284	6	0.0211268	NM_021009	P02248|P02249|P02250|P62988|Q29120|Q6LBL4|Q6LDU5|Q8WYN8|Q91887|Q91888|Q9BWD6|Q9BX98|Q9UEF2|Q9UEG1|Q9UEK8|Q9UPK7	Silent	SNP	ENST00000536769.1	37	CCDS9260.1																																																																																			.	.	none		0.522	UBC-007	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400177.1	NM_021009	
HCN2	610	hgsc.bcm.edu	37	19	603826	603826	+	Silent	SNP	C	C	T	rs56170955	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr19:603826C>T	ENST00000251287.2	+	2	968	c.915C>T	c.(913-915)ttC>ttT	p.F305F		NM_001194.3	NP_001185.3	Q9UL51	HCN2_HUMAN	hyperpolarization activated cyclic nucleotide-gated potassium channel 2	305					cell-cell signaling (GO:0007267)|cellular response to cAMP (GO:0071320)|cellular response to cGMP (GO:0071321)|potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|sodium ion transmembrane transport (GO:0035725)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	cAMP binding (GO:0030552)|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)			endometrium(5)|lung(4)	9		all_epithelial(18;2.78e-22)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;3.55e-06)|all_lung(49;5.41e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		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)		ACTACATCTTCCTTATCGTGG	0.582													c|||	1186	0.236821	0.2368	0.0908	5008	,	,		14018	0.2897		0.0984	False		,,,				2504	0.4284				p.F305F	Melanoma(145;1175 2427 8056 36306)	Atlas-SNP	.											.	HCN2	36	.	0			c.C915T						PASS	.	C		1119,3277		141,837,1220	141.0	108.0	119.0		915	2.8	1.0	19	dbSNP_129	119	900,7698		50,800,3449	no	coding-synonymous	HCN2	NM_001194.3		191,1637,4669	TT,TC,CC		10.4676,25.455,15.5379		305/890	603826	2019,10975	2198	4299	6497	SO:0001819	synonymous_variant	610	exon2			CATCTTCCTTATC	AF064877	CCDS12035.1	19p13	2011-07-05				ENSG00000099822		"""Voltage-gated ion channels / Cyclic nucleotide-regulated channels"""	4846	protein-coding gene	gene with protein product		602781		BCNG2		9405696, 9630217, 16382102	Standard	NM_001194		Approved	BCNG-2, HAC-1	uc002lpe.3	Q9UL51		ENST00000251287.2:c.915C>T	19.37:g.603826C>T		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	65	5	0.0769231	NM_001194	O60742|O60743|O75267|Q9UBS2	Silent	SNP	ENST00000251287.2	37	CCDS12035.1																																																																																			C|0.835;T|0.165	0.165	strong		0.582	HCN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452100.1	NM_001194	
FANCA	2175	hgsc.bcm.edu	37	16	89836323	89836323	+	Missense_Mutation	SNP	C	C	T	rs7195066	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr16:89836323C>T	ENST00000389301.3	-	26	2456	c.2426G>A	c.(2425-2427)gGt>gAt	p.G809D	FANCA_ENST00000567284.2_5'Flank|FANCA_ENST00000568369.1_Missense_Mutation_p.G809D	NM_000135.2	NP_000126.2	O15360	FANCA_HUMAN	Fanconi anemia, complementation group A	809			G -> D (common polymorphism; dbSNP:rs7195066). {ECO:0000269|PubMed:18987736, ECO:0000269|PubMed:9371798, ECO:0000269|PubMed:9399890, ECO:0000269|Ref.4}.		DNA repair (GO:0006281)|female gonad development (GO:0008585)|male gonad development (GO:0008584)|male meiosis (GO:0007140)|protein complex assembly (GO:0006461)|regulation of cell proliferation (GO:0042127)	cytoplasm (GO:0005737)|Fanconi anaemia nuclear complex (GO:0043240)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(5)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(16)|ovary(3)|skin(2)|urinary_tract(3)	47		Lung NSC(15;8.48e-06)|all_lung(18;1.31e-05)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.028)		AAGGCCAGCACCAGGTGCAGG	0.617			"""D, Mis, N, F, S"""			"""AML, leukemia"""		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia				T|||	3339	0.666733	0.7398	0.5821	5008	,	,		17886	0.9881		0.3221	False		,,,				2504	0.6513				p.G809D		Atlas-SNP	.	yes	Rec		Fanconi anaemia A	16	16q24.3	2175	"""Fanconi anemia, complementation group A"""		L	FANCA,NS,carcinoma,0,1	FANCA	99	1	0			c.G2426A						PASS	.	T	ASP/GLY	2895,1501	476.3+/-357.6	953,989,256	92.0	68.0	76.0		2426	-0.2	0.0	16	dbSNP_116	76	2702,5898	682.3+/-403.8	438,1826,2036	yes	missense	FANCA	NM_000135.2	94	1391,2815,2292	TT,TC,CC		31.4186,34.1447,43.0671	benign	809/1456	89836323	5597,7399	2198	4300	6498	SO:0001583	missense	2175	exon26	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	CCAGCACCAGGTG	Z83067	CCDS32515.1, CCDS42221.1, CCDS67099.1	16q24.3	2014-09-17			ENSG00000187741	ENSG00000187741		"""Fanconi anemia, complementation groups"""	3582	protein-coding gene	gene with protein product		607139		FACA, FANCH		7581462, 9382107	Standard	NM_001286167		Approved	FAA, FA-H, FAH	uc002fou.1	O15360		ENST00000389301.3:c.2426G>A	16.37:g.89836323C>T	ENSP00000373952:p.Gly809Asp	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	103	5	0.0485437	NM_000135	A5D923|B4DRI7|H3BSR5|O75266|Q6PL10|Q92497|Q96H18|Q9UEA5|Q9UEL8|Q9UEL9|Q9UPK3|Q9Y6M2	Missense_Mutation	SNP	ENST00000389301.3	37	CCDS32515.1	1344	0.6153846153846154	348	0.7073170731707317	190	0.5248618784530387	565	0.9877622377622378	241	0.3179419525065963	T	3.507	-0.100499	0.06967	0.658553	0.314186	ENSG00000187741	ENST00000389301	D	0.84442	-1.85	3.13	-0.167	0.13347	.	0.597657	0.15671	N	0.250384	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.27054	-1.0085	9	0.18710	T	0.47	-0.0117	2.3692	0.04326	0.1117:0.3478:0.3548:0.1856	rs7195066;rs17233043;rs60022722;rs7195066	809;809	B4DRI7;O15360	.;FANCA_HUMAN	D	809	ENSP00000373952:G809D	ENSP00000373952:G809D	G	-	2	0	FANCA	88363824	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.305000	0.19254	-0.200000	0.10300	-1.562000	0.00884	GGT	C|0.485;T|0.515	0.515	strong		0.617	FANCA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000421927.1		
APOBEC3B	9582	hgsc.bcm.edu	37	22	39381826	39381826	+	Missense_Mutation	SNP	A	A	G	rs2076109	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr22:39381826A>G	ENST00000333467.3	+	3	229	c.184A>G	c.(184-186)Aag>Gag	p.K62E	APOBEC3B_ENST00000402182.3_Missense_Mutation_p.K62E|APOBEC3B_ENST00000407298.3_Missense_Mutation_p.K62E	NM_001270411.1|NM_004900.4	NP_001257340.1|NP_004891	Q9UH17	ABC3B_HUMAN	apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3B	62			K -> E (in dbSNP:rs2076109). {ECO:0000269|PubMed:15461802}.		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)					GGTGTATTTCAAGCCTCAGTA	0.587													C|||	3211	0.641174	0.6762	0.5259	5008	,	,		13686	0.628		0.5974	False		,,,				2504	0.7342				p.K62E		Atlas-SNP	.											.	APOBEC3B	32	.	0			c.A184G						PASS	.	C	GLU/LYS	3020,1374		1091,838,268	107.0	92.0	97.0		184	-1.1	0.0	22	dbSNP_96	97	4829,3735		1532,1765,985	no	missense	APOBEC3B	NM_004900.3	56	2623,2603,1253	GG,GA,AA		43.6128,31.2699,39.4274	benign	62/383	39381826	7849,5109	2197	4282	6479	SO:0001583	missense	9582	exon3			TATTTCAAGCCTC	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.184A>G	22.37:g.39381826A>G	ENSP00000327459:p.Lys62Glu	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	98	9	0.0918367	NM_004900	B0QYD2|O95618|Q20WL1|Q5IFJ4|Q7Z2N3|Q7Z6D6|Q9UE74	Missense_Mutation	SNP	ENST00000333467.3	37	CCDS13982.1	1367	0.6259157509157509	332	0.6747967479674797	185	0.511049723756906	379	0.6625874125874126	471	0.6213720316622692	.	5.287	0.238307	0.10023	0.687301	0.563872	ENSG00000179750	ENST00000407298;ENST00000402182;ENST00000333467	T;T;T	0.65178	-0.14;-0.14;-0.14	0.575	-1.15	0.09709	APOBEC-like, N-terminal (1);Cytidine deaminase-like (1);	.	.	.	.	T	0.00012	0.0000	N	0.25992	0.78	0.80722	P	0.0	B;B	0.18968	0.032;0.0	B;B	0.13407	0.009;0.007	T	0.48514	-0.9029	7	0.19147	T	0.46	.	.	.	.	rs2076109;rs17000716;rs17857431;rs57140217;rs2076109	62;62	B0QYD2;Q9UH17	.;ABC3B_HUMAN	E	62	ENSP00000385068:K62E;ENSP00000385060:K62E;ENSP00000327459:K62E	ENSP00000327459:K62E	K	+	1	0	APOBEC3B	37711772	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.983000	0.01488	-2.941000	0.00297	-2.942000	0.00086	AAG	A|0.388;G|0.612	0.612	strong		0.587	APOBEC3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321233.1	NM_004900	
KRTAP27-1	643812	hgsc.bcm.edu	37	21	31709691	31709691	+	Missense_Mutation	SNP	G	G	A	rs2244485	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr21:31709691G>A	ENST00000382835.2	-	1	321	c.296C>T	c.(295-297)gCg>gTg	p.A99V		NM_001077711.1	NP_001071179.1	Q3LI81	KR271_HUMAN	keratin associated protein 27-1	99			A -> V (in dbSNP:rs2244485).			intermediate filament (GO:0005882)				endometrium(2)|large_intestine(3)|lung(9)|ovary(2)|prostate(1)|skin(1)	18						TGATTGGCACGCTGTCCTTTC	0.502													G|||	1609	0.321286	0.1793	0.3473	5008	,	,		20460	0.2639		0.4503	False		,,,				2504	0.4213				p.A99V		Atlas-SNP	.											KRTAP27-1,NS,carcinoma,-1,1	KRTAP27-1	53	1	0			c.C296T						scavenged	.	G	VAL/ALA	979,3427	367.8+/-318.4	108,763,1332	133.0	133.0	133.0		296	0.3	0.0	21	dbSNP_100	133	4174,4426	568.2+/-389.0	1012,2150,1138	yes	missense	KRTAP27-1	NM_001077711.1	64	1120,2913,2470	AA,AG,GG		48.5349,22.2197,39.6202	benign	99/208	31709691	5153,7853	2203	4300	6503	SO:0001583	missense	643812	exon1			TGGCACGCTGTCC	AB096937	CCDS33532.1	21q22.11	2007-11-23			ENSG00000206107	ENSG00000206107		"""Keratin associated proteins"""	33864	protein-coding gene	gene with protein product							Standard	NM_001077711		Approved		uc002ynx.1	Q3LI81	OTTHUMG00000059577	ENST00000382835.2:c.296C>T	21.37:g.31709691G>A	ENSP00000372286:p.Ala99Val	Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	158	3	0.0189873	NM_001077711		Missense_Mutation	SNP	ENST00000382835.2	37	CCDS33532.1	674	0.3086080586080586	81	0.16463414634146342	127	0.35082872928176795	126	0.2202797202797203	340	0.44854881266490765	G	5.791	0.330292	0.10956	0.222197	0.485349	ENSG00000206107	ENST00000382835	T	0.03301	3.98	4.44	0.262	0.15597	.	2.953730	0.01681	N	0.026127	T	0.00012	0.0000	L	0.36672	1.1	0.80722	P	0.0	P	0.40032	0.699	B	0.32677	0.15	T	0.44019	-0.9355	9	0.34782	T	0.22	2.1633	4.478	0.11753	0.2144:0.3548:0.4308:0.0	rs2244485;rs17593215;rs56539537;rs2244485	99	Q3LI81	KR271_HUMAN	V	99	ENSP00000372286:A99V	ENSP00000372286:A99V	A	-	2	0	KRTAP27-1	30631562	0.003000	0.15002	0.000000	0.03702	0.007000	0.05969	0.536000	0.23129	0.039000	0.15632	0.591000	0.81541	GCG	G|0.654;A|0.346	0.346	strong		0.502	KRTAP27-1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000132470.3	NM_001077711	
MUC2	4583	hgsc.bcm.edu	37	11	1093424	1093424	+	Missense_Mutation	SNP	C	C	G	rs111642532		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr11:1093424C>G	ENST00000441003.2	+	30	5270	c.5243C>G	c.(5242-5244)aCc>aGc	p.T1748S	MUC2_ENST00000333592.6_Missense_Mutation_p.T36S|MUC2_ENST00000359061.5_Missense_Mutation_p.T1715S|MUC2_ENST00000361558.6_Intron	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0					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.T1748S(1)|p.T1715S(1)		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)	acacccatcaccaccaccacc	0.637																																					p.T1748S		Atlas-SNP	.											MUC2_ENST00000441003,NS,carcinoma,0,2	MUC2	614	2	2	Substitution - Missense(2)	prostate(2)	c.C5243G						scavenged	.						207.0	236.0	226.0					11																	1093424		2049	3988	6037	SO:0001583	missense	4583	exon30			CCATCACCACCAC	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.5243C>G	11.37:g.1093424C>G	ENSP00000415183:p.Thr1748Ser	Somatic	67	1	0.0149254		WXS	Illumina HiSeq	Phase_I	64	3	0.046875	NM_002457	Q14878	Missense_Mutation	SNP	ENST00000441003.2	37		.	.	.	.	.	.	.	.	.	.	C	0.295	-0.977665	0.02197	.	.	ENSG00000198788	ENST00000441003;ENST00000359061;ENST00000333592	T;T;T	0.12361	2.69;2.92;2.86	0.891	0.891	0.19224	.	2587.360000	0.00953	N	0.002994	T	0.11324	0.0276	.	.	.	0.09310	N	1	B	0.26876	0.162	B	0.17979	0.02	T	0.28681	-1.0036	9	0.49607	T	0.09	.	7.6247	0.28206	0.0:1.0:0.0:0.0	.	1748	E7EUV1	.	S	1748;1715;36	ENSP00000415183:T1748S;ENSP00000351956:T1715S;ENSP00000331373:T36S	ENSP00000331373:T36S	T	+	2	0	MUC2	1083424	0.000000	0.05858	0.003000	0.11579	0.004000	0.04260	0.014000	0.13333	0.801000	0.34066	0.195000	0.17529	ACC	C|0.500;G|0.500	0.500	weak		0.637	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
CST9L	128821	hgsc.bcm.edu	37	20	23546639	23546639	+	Missense_Mutation	SNP	T	T	G	rs2295564	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr20:23546639T>G	ENST00000376979.3	-	2	624	c.326A>C	c.(325-327)cAt>cCt	p.H109P		NM_080610.2	NP_542177.1	Q9H4G1	CST9L_HUMAN	cystatin 9-like	109			H -> P (in dbSNP:rs2295564).			extracellular region (GO:0005576)	cysteine-type endopeptidase inhibitor activity (GO:0004869)	p.H109P(1)		breast(1)|endometrium(1)|large_intestine(1)|lung(4)|prostate(1)	8	Colorectal(13;0.0431)|Lung NSC(19;0.235)					TTCTTGGAAATGGCAGTTGTC	0.502													G|||	1882	0.375799	0.1899	0.4049	5008	,	,		22065	0.5417		0.3877	False		,,,				2504	0.4233				p.H109P		Atlas-SNP	.											CST9L,NS,carcinoma,0,1	CST9L	25	1	1	Substitution - Missense(1)	prostate(1)	c.A326C						scavenged	.	G	PRO/HIS	997,3409	730.4+/-410.2	128,741,1334	285.0	228.0	247.0		326	1.9	0.2	20	dbSNP_100	247	3511,5089	633.0+/-398.7	710,2091,1499	yes	missense	CST9L	NM_080610.2	77	838,2832,2833	GG,GT,TT		40.8256,22.6282,34.6609	benign	109/148	23546639	4508,8498	2203	4300	6503	SO:0001583	missense	128821	exon2			TGGAAATGGCAGT		CCDS13157.1	20p11.21	2012-08-14	2008-03-06		ENSG00000101435	ENSG00000101435			16233	protein-coding gene	gene with protein product			"""cystatin 9 (mouse)-like"""			20565543	Standard	NM_080610		Approved	bA218C14.1, CTES7B	uc002wtk.4	Q9H4G1	OTTHUMG00000032073	ENST00000376979.3:c.326A>C	20.37:g.23546639T>G	ENSP00000366178:p.His109Pro	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	111	4	0.036036	NM_080610	B2R5A1	Missense_Mutation	SNP	ENST00000376979.3	37	CCDS13157.1	839	0.3841575091575092	89	0.18089430894308944	153	0.42265193370165743	305	0.5332167832167832	292	0.38522427440633245	G	0.007	-1.937714	0.00484	0.226282	0.408256	ENSG00000101435	ENST00000376979	T	0.24350	1.86	1.92	1.92	0.25849	Proteinase inhibitor I25, cystatin (2);	0.000000	0.37261	N	0.002175	T	0.00012	0.0000	N	0.00016	-2.85	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.45220	-0.9276	9	0.02654	T	1	.	5.6793	0.17765	0.0:0.0:0.6787:0.3213	rs2295564;rs17231619;rs52819629;rs2295564	109	Q9H4G1	CST9L_HUMAN	P	109	ENSP00000366178:H109P	ENSP00000366178:H109P	H	-	2	0	CST9L	23494639	0.711000	0.27906	0.202000	0.23494	0.040000	0.13550	0.460000	0.21924	0.363000	0.24346	-0.323000	0.08544	CAT	T|0.629;G|0.371	0.371	strong		0.502	CST9L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078338.1	NM_080610	
EMC1	23065	hgsc.bcm.edu	37	1	19565344	19565344	+	Missense_Mutation	SNP	C	C	G	rs709683	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr1:19565344C>G	ENST00000477853.1	-	10	1076	c.1034G>C	c.(1033-1035)aGt>aCt	p.S345T	EMC1_ENST00000375208.3_Missense_Mutation_p.S323T|EMC1_ENST00000375199.3_Missense_Mutation_p.S344T|RP1-43E13.2_ENST00000437898.1_RNA	NM_001271427.1|NM_001271428.1|NM_015047.2	NP_001258356.1|NP_001258357.1|NP_055862.1	Q8N766	EMC1_HUMAN	ER membrane protein complex subunit 1	345			S -> T (in dbSNP:rs709683). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:16303743}.			ER membrane protein complex (GO:0072546)|integral component of membrane (GO:0016021)											AGAACTGCTACTTTTCTGCTA	0.458													G|||	2866	0.572284	0.7315	0.5101	5008	,	,		18872	0.7401		0.3469	False		,,,				2504	0.4601				p.S345T		Atlas-SNP	.											.	.	.	.	0			c.G1034C						PASS	.	G	THR/SER	3012,1394	458.0+/-351.8	1047,918,238	116.0	124.0	121.0		1034	5.2	0.9	1	dbSNP_86	121	3095,5505	659.4+/-401.7	566,1963,1771	yes	missense	KIAA0090	NM_015047.1	58	1613,2881,2009	GG,GC,CC		35.9884,31.6387,46.9553	benign	345/994	19565344	6107,6899	2203	4300	6503	SO:0001583	missense	23065	exon10			CTGCTACTTTTCT		CCDS190.1, CCDS59190.1, CCDS59191.1	1p36.13	2012-05-23	2012-05-23	2012-05-23	ENSG00000127463	ENSG00000127463			28957	protein-coding gene	gene with protein product			"""KIAA0090"""	KIAA0090		22119785	Standard	NM_015047		Approved		uc001bbo.4	Q8N766	OTTHUMG00000002497	ENST00000477853.1:c.1034G>C	1.37:g.19565344C>G	ENSP00000420608:p.Ser345Thr	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	112	5	0.0446429	NM_001271428	A8K6F3|Q14700|Q5TG62|Q63HL0|Q63HL3|Q8NBH8	Missense_Mutation	SNP	ENST00000477853.1	37	CCDS190.1	1224|1224	0.5604395604395604|0.5604395604395604	361|361	0.733739837398374|0.733739837398374	167|167	0.4613259668508287|0.4613259668508287	431|431	0.7534965034965035|0.7534965034965035	265|265	0.3496042216358839|0.3496042216358839	G|G	7.688|7.688	0.690412|0.690412	0.15039|0.15039	0.683613|0.683613	0.359884|0.359884	ENSG00000127463|ENSG00000127463	ENST00000375197|ENST00000477853;ENST00000375199;ENST00000375208	.|T;T;T	.|0.23147	.|1.98;1.92;1.98	6.17|6.17	5.22|5.22	0.72569|0.72569	.|.	.|0.708347	.|0.15080	.|N	.|0.281698	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.08118|0.08118	0|0	0.58432|0.58432	P|P	4.000000000004E-6|4.000000000004E-6	.|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|T	0.16217|0.16217	-1.0410|-1.0410	5|9	0.39692|0.12430	T|T	0.17|0.62	-7.2019|-7.2019	16.2834|16.2834	0.82708|0.82708	0.0:0.2663:0.7337:0.0|0.0:0.2663:0.7337:0.0	rs709683;rs57408009;rs709683|rs709683;rs57408009;rs709683	.|323;344;345;345	.|Q8N766-4;Q8N766-2;Q8N766-3;Q8N766	.|.;.;.;K0090_HUMAN	N|T	78|345;344;323	.|ENSP00000420608:S345T;ENSP00000364345:S344T;ENSP00000364354:S323T	ENSP00000364343:K78N|ENSP00000364345:S344T	K|S	-|-	3|2	2|0	KIAA0090|KIAA0090	19437931|19437931	0.934000|0.934000	0.31675|0.31675	0.868000|0.868000	0.34077|0.34077	0.804000|0.804000	0.45430|0.45430	2.667000|2.667000	0.46808|0.46808	1.643000|1.643000	0.50594|0.50594	-0.120000|-0.120000	0.15030|0.15030	AAG|AGT	C|0.506;G|0.494	0.494	strong		0.458	EMC1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000007076.2	NM_015047	
SLITRK2	84631	hgsc.bcm.edu	37	X	144905286	144905286	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chrX:144905286G>A	ENST00000370490.1	+	1	5598	c.1343G>A	c.(1342-1344)aGc>aAc	p.S448N	SLITRK2_ENST00000428560.2_Missense_Mutation_p.S448N|SLITRK2_ENST00000447897.2_Missense_Mutation_p.S448N|SLITRK2_ENST00000434188.2_Missense_Mutation_p.S448N|SLITRK2_ENST00000413937.2_Missense_Mutation_p.S448N			Q9H156	SLIK2_HUMAN	SLIT and NTRK-like family, member 2	448					axonogenesis (GO:0007409)	integral component of membrane (GO:0016021)		p.S448I(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(9)|kidney(1)|large_intestine(17)|lung(40)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	86	Acute lymphoblastic leukemia(192;6.56e-05)					GGACTGCAGAGCTTGCAATAT	0.393																																					p.S448N		Atlas-SNP	.											.	SLITRK2	221	.	1	Substitution - Missense(1)	lung(1)	c.G1343A						PASS	.						137.0	142.0	140.0					X																	144905286		2203	4300	6503	SO:0001583	missense	84631	exon5			TGCAGAGCTTGCA	Y19205	CCDS14680.1	Xq27.3	2008-02-05	2004-03-11		ENSG00000185985	ENSG00000185985			13449	protein-coding gene	gene with protein product		300561	"""slit-like 1 (Drosophila)"""	SLITL1		11347906, 14557068	Standard	NM_032539		Approved	KIAA1854, CXorf2	uc011mwr.2	Q9H156	OTTHUMG00000022595	ENST00000370490.1:c.1343G>A	X.37:g.144905286G>A	ENSP00000359521:p.Ser448Asn	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	120	37	0.308333	NM_001144005	A8K117|Q2KHN3|Q5JXB1|Q8NBC7|Q96JH3	Missense_Mutation	SNP	ENST00000370490.1	37	CCDS14680.1	.	.	.	.	.	.	.	.	.	.	G	10.42	1.344294	0.24339	.	.	ENSG00000185985	ENST00000335565;ENST00000447897;ENST00000370490;ENST00000434188;ENST00000413937;ENST00000428560	T;T;T;T;T;T	0.60672	0.17;0.17;0.17;0.17;0.17;0.17	5.5	5.5	0.81552	.	0.207561	0.46758	D	0.000261	T	0.39545	0.1082	N	0.05078	-0.115	0.50313	D	0.999865	P	0.40066	0.701	P	0.44946	0.465	T	0.39961	-0.9588	10	0.02654	T	1	-11.1755	15.6243	0.76840	0.0:0.0:1.0:0.0	.	448	Q9H156	SLIK2_HUMAN	N	448	ENSP00000334374:S448N;ENSP00000411681:S448N;ENSP00000359521:S448N;ENSP00000397015:S448N;ENSP00000407347:S448N;ENSP00000412010:S448N	ENSP00000334374:S448N	S	+	2	0	SLITRK2	144712978	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.233000	0.72320	2.285000	0.76669	0.600000	0.82982	AGC	.	.	none		0.393	SLITRK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058633.1	NM_032539	
AQP7	364	hgsc.bcm.edu	37	9	33395103	33395103	+	Silent	SNP	G	G	A	rs148012859		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr9:33395103G>A	ENST00000539936.1	-	3	355	c.117C>T	c.(115-117)gcC>gcT	p.A39A	AQP7_ENST00000541274.1_5'UTR|AQP7_ENST00000377425.4_Intron|AQP7_ENST00000537089.1_5'UTR			O14520	AQP7_HUMAN	aquaporin 7	39					excretion (GO:0007588)|generation of precursor metabolites and energy (GO:0006091)|glycerol transport (GO:0015793)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	glycerol channel activity (GO:0015254)|water channel activity (GO:0015250)	p.A39A(1)		NS(1)|large_intestine(1)|lung(7)|ovary(1)|prostate(4)|skin(2)|stomach(1)	17			LUSC - Lung squamous cell carcinoma(29;0.00788)	GBM - Glioblastoma multiforme(74;0.191)		TCATGAACTCGGCCAGGAACT	0.582																																					p.A39A		Atlas-SNP	.											AQP7,NS,carcinoma,0,1	AQP7	58	1	1	Substitution - coding silent(1)	prostate(1)	c.C117T						scavenged	.						126.0	85.0	99.0					9																	33395103		2203	4300	6503	SO:0001819	synonymous_variant	364	exon3			GAACTCGGCCAGG	AB006190	CCDS6541.1	9p13	2008-02-05			ENSG00000165269	ENSG00000165269		"""Ion channels / Aquaporins"""	640	protein-coding gene	gene with protein product		602974		AQP7L		9252401	Standard	NM_001170		Approved	AQP9, AQPap	uc003zst.3	O14520	OTTHUMG00000019773	ENST00000539936.1:c.117C>T	9.37:g.33395103G>A		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	105	3	0.0285714	NM_001170	Q08E94|Q5T5L9|Q8NHM3	Silent	SNP	ENST00000539936.1	37																																																																																				A|0.002;G|0.998;T|0.000	0.002	strong		0.582	AQP7-203	KNOWN	basic	protein_coding	protein_coding		NM_001170	
SENP1	29843	hgsc.bcm.edu	37	12	48477422	48477422	+	Silent	SNP	A	A	G	rs886588	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr12:48477422A>G	ENST00000004980.5	-	6	982	c.504T>C	c.(502-504)ctT>ctC	p.L168L	SENP1_ENST00000549518.1_Silent_p.L168L|SENP1_ENST00000448372.1_Silent_p.L168L|SENP1_ENST00000547886.1_5'UTR|SENP1_ENST00000339976.6_3'UTR|RNU6-1203P_ENST00000410703.1_RNA|SENP1_ENST00000549595.1_Silent_p.L168L|SENP1_ENST00000551330.1_Silent_p.L168L			Q9P0U3	SENP1_HUMAN	SUMO1/sentrin specific peptidase 1	168	Ser-rich.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic signaling pathway (GO:0097190)|cellular protein metabolic process (GO:0044267)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-translational protein modification (GO:0043687)|protein desumoylation (GO:0016926)|protein sumoylation (GO:0016925)|proteolysis (GO:0006508)|regulation of definitive erythrocyte differentiation (GO:0010724)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	endopeptidase activity (GO:0004175)|SUMO-specific protease activity (GO:0016929)	p.L168L(1)		large_intestine(3)|lung(1)|pancreas(2)|stomach(1)	7		Acute lymphoblastic leukemia(13;0.108)|all_hematologic(14;0.214)				TGGGGCTCAAAAGACTTCGAC	0.408													A|||	803	0.160343	0.053	0.1744	5008	,	,		18083	0.2371		0.2177	False		,,,				2504	0.1575				p.L168L		Atlas-SNP	.											SENP1,NS,carcinoma,0,1	SENP1	44	1	1	Substitution - coding silent(1)	stomach(1)	c.T504C						scavenged	.	A		253,3463		11,231,1616	120.0	111.0	114.0		504	1.8	1.0	12	dbSNP_86	114	1803,6381		192,1419,2481	no	coding-synonymous	SENP1	NM_014554.2		203,1650,4097	GG,GA,AA		22.0308,6.8084,17.2773		168/644	48477422	2056,9844	1858	4092	5950	SO:0001819	synonymous_variant	29843	exon6			GCTCAAAAGACTT	AF149770	CCDS44868.1, CCDS44868.2	12q13.1	2008-02-05	2005-08-17			ENSG00000079387			17927	protein-coding gene	gene with protein product		612157	"""SUMO1/sentrin specific protease 1"""			10652325, 14563852	Standard	NM_001267595		Approved		uc009zkx.4	Q9P0U3	OTTHUMG00000169896	ENST00000004980.5:c.504T>C	12.37:g.48477422A>G		Somatic	112	1	0.00892857		WXS	Illumina HiSeq	Phase_I	140	2	0.0142857	NM_001267594	A8K7P5|Q86XC8	Silent	SNP	ENST00000004980.5	37	CCDS44868.2																																																																																			A|0.817;G|0.183	0.183	strong		0.408	SENP1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000406471.1	NM_014554	
UNC5CL	222643	hgsc.bcm.edu	37	6	40998141	40998141	+	Silent	SNP	G	G	A	rs736795	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr6:40998141G>A	ENST00000373164.1	-	7	1380	c.1320C>T	c.(1318-1320)tgC>tgT	p.C440C	UNC5CL_ENST00000470102.1_5'UTR|UNC5CL_ENST00000244565.3_Silent_p.C440C			Q8IV45	UN5CL_HUMAN	unc-5 homolog C (C. elegans)-like	440	Death. {ECO:0000255|PROSITE- ProRule:PRU00064}.				positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of JNK cascade (GO:0046330)|proteolysis (GO:0006508)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	peptidase activity (GO:0008233)			endometrium(1)|kidney(3)|large_intestine(3)|lung(3)|ovary(2)|upper_aerodigestive_tract(1)	13	Ovarian(28;0.0418)|Colorectal(47;0.196)					TCTTCATGCCGCAAAGCCCCA	0.597													G|||	1385	0.276558	0.2368	0.268	5008	,	,		19416	0.2778		0.2038	False		,,,				2504	0.41				p.C440C		Atlas-SNP	.											.	UNC5CL	52	.	0			c.C1320T						PASS	.	G		1033,3373	380.9+/-323.9	131,771,1301	82.0	74.0	76.0		1320	-5.8	0.9	6	dbSNP_86	76	2098,6502	363.7+/-333.3	254,1590,2456	no	coding-synonymous	UNC5CL	NM_173561.2		385,2361,3757	AA,AG,GG		24.3953,23.4453,24.0735		440/519	40998141	3131,9875	2203	4300	6503	SO:0001819	synonymous_variant	222643	exon8			CATGCCGCAAAGC	BC035284	CCDS4847.1	6p21.1	2013-10-15			ENSG00000124602	ENSG00000124602			21203	protein-coding gene	gene with protein product	"""ZU5 and death domain containing"""					14769797	Standard	NM_173561		Approved	MGC34763, ZUD	uc003opi.3	Q8IV45	OTTHUMG00000014665	ENST00000373164.1:c.1320C>T	6.37:g.40998141G>A		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	99	5	0.050505	NM_173561	Q5TGU1	Silent	SNP	ENST00000373164.1	37	CCDS4847.1																																																																																			G|0.767;A|0.233	0.233	strong		0.597	UNC5CL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040491.1	NM_173561	
CCDC180	100499483	hgsc.bcm.edu	37	9	100122291	100122291	+	Missense_Mutation	SNP	T	T	C	rs3747495	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr9:100122291T>C	ENST00000357054.1	+	37	4371	c.3436T>C	c.(3436-3438)Ttc>Ctc	p.F1146L	CCDC180_ENST00000375202.2_Missense_Mutation_p.F1175L|CCDC180_ENST00000529487.1_Missense_Mutation_p.F1175L|RP11-23J9.4_ENST00000534123.1_RNA|CCDC180_ENST00000395220.1_3'UTR			Q9P1Z9	CC180_HUMAN	coiled-coil domain containing 180	1146			F -> L (in dbSNP:rs3747495).			extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)		p.F1146L(1)									ACTCCTCAGCTTCGTCCAAAC	0.507													T|||	1159	0.23143	0.1369	0.3444	5008	,	,		21733	0.2907		0.1879	False		,,,				2504	0.2628				p.F1175L		Atlas-SNP	.											KIAA1529,NS,carcinoma,0,1	.	.	1	1	Substitution - Missense(1)	stomach(1)	c.T3523C						scavenged	.	T	LEU/PHE	618,3788	267.7+/-268.0	42,534,1627	166.0	166.0	166.0		3523	3.4	0.0	9	dbSNP_107	166	1588,7012	298.5+/-303.9	142,1304,2854	yes	missense	C9orf174	NM_020893.2	22	184,1838,4481	CC,CT,TT		18.4651,14.0263,16.9614	benign	1175/1702	100122291	2206,10800	2203	4300	6503	SO:0001583	missense	0	exon26			CTCAGCTTCGTCC	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.3436T>C	9.37:g.100122291T>C	ENSP00000349562:p.Phe1146Leu	Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	148	5	0.0337838	NM_020893	Q2KHR6|Q5VV25|Q68DP5|Q69YV9|Q6AHY0	Missense_Mutation	SNP	ENST00000357054.1	37		508	0.2326007326007326	52	0.10569105691056911	128	0.35359116022099446	174	0.3041958041958042	154	0.20316622691292877	T	12.99	2.103262	0.37145	0.140263	0.184651	ENSG00000197816	ENST00000357054;ENST00000375202;ENST00000529487	T;T;T	0.08102	3.13;3.15;3.15	5.71	3.39	0.38822	.	0.472963	0.25919	N	0.027445	T	0.00012	0.0000	L	0.27053	0.805	0.54753	P	1.0999999999983245E-5	B;B	0.33637	0.119;0.42	B;B	0.32090	0.097;0.14	T	0.45366	-0.9266	9	0.10377	T	0.69	-2.0155	6.8103	0.23801	0.0:0.192:0.0:0.808	rs3747495;rs13302501;rs17583370;rs52794397;rs61215609;rs3747495	1314;1146	B7ZMG3;Q9P1Z9	.;CI174_HUMAN	L	1146;1175;1175	ENSP00000349562:F1146L;ENSP00000364348:F1175L;ENSP00000434727:F1175L	ENSP00000349562:F1146L	F	+	1	0	C9orf174	99162112	0.676000	0.27567	0.002000	0.10522	0.031000	0.12232	1.588000	0.36633	0.544000	0.28883	0.459000	0.35465	TTC	T|0.807;C|0.193	0.193	strong		0.507	CCDC180-201	KNOWN	basic	protein_coding	protein_coding		NM_020893	
WDR91	29062	hgsc.bcm.edu	37	7	134880931	134880931	+	Silent	SNP	C	C	T	rs2288240	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr7:134880931C>T	ENST00000354475.4	-	8	1240	c.1209G>A	c.(1207-1209)gaG>gaA	p.E403E	WDR91_ENST00000423565.1_Silent_p.E368E|AC009542.2_ENST00000412549.2_RNA|WDR91_ENST00000485942.1_5'Flank|WDR91_ENST00000344400.5_Silent_p.E403E	NM_014149.3	NP_054868.3	A4D1P6	WDR91_HUMAN	WD repeat domain 91	403										breast(3)|endometrium(2)|kidney(2)|large_intestine(12)|lung(14)|ovary(1)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)	40						GTTCCCCGTACTCCTCCTGTC	0.622													C|||	286	0.0571086	0.0	0.0331	5008	,	,		17252	0.2093		0.002	False		,,,				2504	0.0511				p.E403E		Atlas-SNP	.											.	WDR91	82	.	0			c.G1209A						PASS	.	C		9,4397	15.5+/-35.6	0,9,2194	80.0	79.0	79.0		1209	4.9	1.0	7	dbSNP_100	79	20,8580	14.0+/-48.4	0,20,4280	no	coding-synonymous	WDR91	NM_014149.3		0,29,6474	TT,TC,CC		0.2326,0.2043,0.223		403/748	134880931	29,12977	2203	4300	6503	SO:0001819	synonymous_variant	29062	exon8			CCCGTACTCCTCC	AF161534	CCDS34758.1	7q33	2013-01-09			ENSG00000105875	ENSG00000105875		"""WD repeat domain containing"""	24997	protein-coding gene	gene with protein product						11042152, 11230166	Standard	NM_014149		Approved	HSPC049	uc003vsp.2	A4D1P6	OTTHUMG00000155414	ENST00000354475.4:c.1209G>A	7.37:g.134880931C>T		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	95	4	0.0421053	NM_014149	A6NK54|C9JMI4|Q6FI65|Q6MZQ1|Q6P4I1|Q96AE5|Q96G63|Q9H062|Q9H9B6|Q9NVG7|Q9NZY6	Silent	SNP	ENST00000354475.4	37	CCDS34758.1																																																																																			C|0.966;T|0.034	0.034	strong		0.622	WDR91-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340019.1	NM_014149	
CEP131	22994	hgsc.bcm.edu	37	17	79173545	79173545	+	Missense_Mutation	SNP	G	G	T			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr17:79173545G>T	ENST00000269392.4	-	9	1244	c.997C>A	c.(997-999)Cgc>Agc	p.R333S	RP11-455O6.2_ENST00000571085.1_RNA|AZI1_ENST00000575907.1_Missense_Mutation_p.R333S|AZI1_ENST00000570482.2_5'Flank|AZI1_ENST00000450824.2_Missense_Mutation_p.R333S|AZI1_ENST00000374782.3_Missense_Mutation_p.R333S	NM_014984.2	NP_055799.2	Q9UPN4	CP131_HUMAN		333					cell differentiation (GO:0030154)|G2/M transition of mitotic cell cycle (GO:0000086)|intraciliary transport involved in cilium morphogenesis (GO:0035735)|mitotic cell cycle (GO:0000278)|multicellular organismal development (GO:0007275)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular protein transport (GO:0090316)|regulation of centrosome duplication (GO:0010824)|spermatogenesis (GO:0007283)	BBSome (GO:0034464)|cell projection (GO:0042995)|centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)	protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(3)|endometrium(6)|kidney(3)|large_intestine(1)|lung(12)|ovary(2)|prostate(3)|urinary_tract(5)	36	all_neural(118;0.0804)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0272)|OV - Ovarian serous cystadenocarcinoma(97;0.117)			CTGGCTTGGCGTGCCTTCTCC	0.692																																					p.R333S		Atlas-SNP	.											.	AZI1	145	.	0			c.C997A						PASS	.						63.0	56.0	58.0					17																	79173545		2201	4297	6498	SO:0001583	missense	22994	exon9			CTTGGCGTGCCTT																												ENST00000269392.4:c.997C>A	17.37:g.79173545G>T	ENSP00000269392:p.Arg333Ser	Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	45	4	0.0888889	NM_014984	A6NHI8|B2RN11|Q96F50	Missense_Mutation	SNP	ENST00000269392.4	37		.	.	.	.	.	.	.	.	.	.	G	17.28	3.349810	0.61183	.	.	ENSG00000141577	ENST00000450824;ENST00000374782;ENST00000269392	T;T;T	0.26518	1.73;1.73;1.73	3.67	3.67	0.42095	.	0.060253	0.64402	D	0.000002	T	0.48732	0.1516	M	0.70275	2.135	0.51012	D	0.999904	D;D;D;D	0.76494	0.997;0.997;0.999;0.969	D;D;D;P	0.68765	0.917;0.917;0.96;0.806	T	0.56329	-0.7997	10	0.72032	D	0.01	-13.0848	15.5205	0.75862	0.0:0.0:1.0:0.0	.	333;333;333;333	B2RN10;Q9UPN4;Q9UPN4-3;Q9UPN4-2	.;AZI1_HUMAN;.;.	S	333	ENSP00000393583:R333S;ENSP00000363914:R333S;ENSP00000269392:R333S	ENSP00000269392:R333S	R	-	1	0	AZI1	76788140	1.000000	0.71417	0.916000	0.36221	0.034000	0.12701	5.139000	0.64801	2.038000	0.60285	0.313000	0.20887	CGC	.	.	none		0.692	AZI1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000256070.1		
ZNF799	90576	hgsc.bcm.edu	37	19	12501907	12501907	+	Silent	SNP	A	A	G	rs556226523	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr19:12501907A>G	ENST00000430385.3	-	4	1505	c.1305T>C	c.(1303-1305)tcT>tcC	p.S435S	CTD-3105H18.14_ENST00000435033.1_Intron|ZNF799_ENST00000419318.1_Silent_p.S403S	NM_001080821.2	NP_001074290.1	Q96GE5	ZN799_HUMAN	zinc finger protein 799	435					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)|kidney(2)|large_intestine(4)|lung(4)|ovary(2)|prostate(2)|skin(2)	19						GCCTTCGAAGAGAACTGGAAA	0.368													A|||	35	0.00698882	0.0166	0.0	5008	,	,		23529	0.0		0.003	False		,,,				2504	0.0102				p.S435S		Atlas-SNP	.											ZNF799_ENST00000430385,NS,carcinoma,0,2	ZNF799	111	2	0			c.T1305C						scavenged	.						101.0	104.0	103.0					19																	12501907		2203	4300	6503	SO:0001819	synonymous_variant	90576	exon4			TCGAAGAGAACTG	BC009517	CCDS45989.1	19p13.2	2013-01-08			ENSG00000196466	ENSG00000196466		"""Zinc fingers, C2H2-type"", ""-"""	28071	protein-coding gene	gene with protein product			"""zinc finger protein 842"""	ZNF842			Standard	NM_001080821		Approved	HIT-40, MGC71805	uc002mts.4	Q96GE5	OTTHUMG00000156408	ENST00000430385.3:c.1305T>C	19.37:g.12501907A>G		Somatic	145	3	0.0206897		WXS	Illumina HiSeq	Phase_I	125	7	0.056	NM_001080821		Silent	SNP	ENST00000430385.3	37	CCDS45989.1																																																																																			.	.	none		0.368	ZNF799-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344099.2	NM_001080821	
FAM200B	285550	hgsc.bcm.edu	37	4	15689632	15689632	+	Silent	SNP	G	G	A	rs11729955	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr4:15689632G>A	ENST00000422728.2	+	2	1870	c.1032G>A	c.(1030-1032)gaG>gaA	p.E344E	FAM200B_ENST00000504137.1_Intron	NM_001145191.1	NP_001138663.1	P0CF97	F200B_HUMAN	family with sequence similarity 200, member B	344							nucleic acid binding (GO:0003676)	p.E344E(2)		endometrium(1)|kidney(1)	2						atctcatggaggtattgaaaa	0.328													A|||	1502	0.29992	0.3858	0.3098	5008	,	,		17540	0.1379		0.4056	False		,,,				2504	0.2352				p.E344E		Atlas-SNP	.											FAM200B_ENST00000422728,NS,carcinoma,0,2	FAM200B	56	2	2	Substitution - coding silent(2)	kidney(2)	c.G1032A						scavenged	.	A		529,855		110,309,273	52.0	48.0	49.0		1032	2.6	1.0	4	dbSNP_120	49	1257,1925		249,759,583	no	coding-synonymous	FAM200B	NM_001145191.1		359,1068,856	AA,AG,GG		39.5035,38.2225,39.1152		344/658	15689632	1786,2780	692	1591	2283	SO:0001819	synonymous_variant	285550	exon2			CATGGAGGTATTG	BC048993	CCDS47028.1	4p15.32	2014-04-02			ENSG00000237765	ENSG00000237765			27740	protein-coding gene	gene with protein product	"""chromosome 4 open reading frame 53"""						Standard	NM_001145191		Approved	C4orf53	uc003gof.4	P0CF97	OTTHUMG00000160279	ENST00000422728.2:c.1032G>A	4.37:g.15689632G>A		Somatic	421	1	0.0023753		WXS	Illumina HiSeq	Phase_I	425	9	0.0211765	NM_001145191		Silent	SNP	ENST00000422728.2	37	CCDS47028.1																																																																																			G|0.683;A|0.317	0.317	strong		0.328	FAM200B-005	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360100.1	NM_001145191	
PJA2	9867	hgsc.bcm.edu	37	5	108672946	108672946	+	Missense_Mutation	SNP	C	C	T	rs246105	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr5:108672946C>T	ENST00000361189.2	-	10	2352	c.2113G>A	c.(2113-2115)Gca>Aca	p.A705T	PJA2_ENST00000361557.3_Missense_Mutation_p.A705T	NM_014819.4	NP_055634.3	O43164	PJA2_HUMAN	praja ring finger 2, E3 ubiquitin protein ligase	705	Interaction with PRKAR1A, PRKAR2A and PRKAR2B.		A -> T (in dbSNP:rs246105).		long-term memory (GO:0007616)|protein ubiquitination (GO:0016567)|regulation of protein kinase A signaling (GO:0010738)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	ligase activity (GO:0016874)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(2)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	21		all_cancers(142;4.4e-06)|all_epithelial(76;8.17e-08)|Prostate(80;0.00676)|Lung NSC(167;0.0436)|Ovarian(225;0.0443)|all_lung(232;0.053)|Colorectal(57;0.0946)|Breast(839;0.151)		OV - Ovarian serous cystadenocarcinoma(64;3.46e-10)|Epithelial(69;6.02e-09)|COAD - Colon adenocarcinoma(37;0.224)		GGTGCTTCTGCAATACTGTCA	0.423													C|||	1497	0.298922	0.1172	0.2781	5008	,	,		14077	0.5565		0.2475	False		,,,				2504	0.3466				p.A705T		Atlas-SNP	.											.	PJA2	53	.	0			c.G2113A						PASS	.	C	THR/ALA	713,3691	293.8+/-282.8	67,579,1556	100.0	97.0	98.0		2113	0.4	0.0	5	dbSNP_79	98	2016,6584	352.2+/-328.6	242,1532,2526	yes	missense	PJA2	NM_014819.4	58	309,2111,4082	TT,TC,CC		23.4419,16.1898,20.9859	benign	705/709	108672946	2729,10275	2202	4300	6502	SO:0001583	missense	9867	exon10			CTTCTGCAATACT	AB007898	CCDS4099.1	5q22.1	2013-01-09	2012-02-23	2003-06-05	ENSG00000198961	ENSG00000198961		"""RING-type (C3HC4) zinc fingers"""	17481	protein-coding gene	gene with protein product			"""ring finger protein 131"", ""praja ring finger 2"""	RNF131			Standard	NM_014819		Approved	KIAA0438, Neurodap1	uc003kos.4	O43164	OTTHUMG00000128750	ENST00000361189.2:c.2113G>A	5.37:g.108672946C>T	ENSP00000354775:p.Ala705Thr	Somatic	256	0	0		WXS	Illumina HiSeq	Phase_I	228	16	0.0701754	NM_014819	A8K6U4|D3DSZ5|Q68D49|Q8N1G5	Missense_Mutation	SNP	ENST00000361189.2	37	CCDS4099.1	687	0.31456043956043955	64	0.13008130081300814	96	0.26519337016574585	338	0.5909090909090909	189	0.24934036939313983	C	12.36	1.913297	0.33815	0.161898	0.234419	ENSG00000198961	ENST00000361189;ENST00000361557	T;T	0.11169	2.8;2.8	5.9	0.451	0.16629	.	0.691756	0.13453	N	0.386738	T	0.00012	0.0000	N	0.08118	0	0.51482	P	7.299999999998974E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.30475	-0.9977	9	0.48119	T	0.1	-5.7798	3.7465	0.08549	0.2706:0.3504:0.0:0.379	rs246105;rs17292734;rs17745933;rs58995813;rs246105	705	O43164	PJA2_HUMAN	T	705	ENSP00000354775:A705T;ENSP00000355284:A705T	ENSP00000354775:A705T	A	-	1	0	PJA2	108700845	0.225000	0.23685	0.026000	0.17262	0.307000	0.27823	0.041000	0.13927	0.125000	0.18397	0.650000	0.86243	GCA	C|0.735;T|0.265	0.265	strong		0.423	PJA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250663.1	NM_014819	
MUC6	4588	hgsc.bcm.edu	37	11	1017974	1017974	+	Missense_Mutation	SNP	C	C	G	rs200353019		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr11:1017974C>G	ENST00000421673.2	-	31	4877	c.4827G>C	c.(4825-4827)caG>caC	p.Q1609H		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	1609	Approximate repeats.|Pro-rich.|Thr-rich.				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)	p.Q1609H(2)		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)		GAAGTGTGGTCTGAGGGTGTG	0.547																																					p.Q1609H		Atlas-SNP	.											MUC6_ENST00000421673,colon,carcinoma,0,2	MUC6	408	2	2	Substitution - Missense(2)	large_intestine(2)	c.G4827C						scavenged	.						473.0	441.0	452.0					11																	1017974		2186	4282	6468	SO:0001583	missense	4588	exon31			TGTGGTCTGAGGG	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.4827G>C	11.37:g.1017974C>G	ENSP00000406861:p.Gln1609His	Somatic	345	4	0.0115942		WXS	Illumina HiSeq	Phase_I	395	8	0.0202532	NM_005961	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	Missense_Mutation	SNP	ENST00000421673.2	37	CCDS44513.1	.	.	.	.	.	.	.	.	.	.	C	5.277	0.236564	0.10023	.	.	ENSG00000184956	ENST00000421673	T	0.35421	1.31	2.39	0.333	0.15943	.	.	.	.	.	T	0.26702	0.0653	L	0.52011	1.625	0.09310	N	1	B	0.25486	0.127	B	0.27715	0.082	T	0.28681	-1.0036	9	0.22109	T	0.4	.	3.4702	0.07565	0.0:0.5042:0.2173:0.2785	.	1609	Q6W4X9	MUC6_HUMAN	H	1609	ENSP00000406861:Q1609H	ENSP00000406861:Q1609H	Q	-	3	2	MUC6	1007974	0.000000	0.05858	0.003000	0.11579	0.027000	0.11550	-2.394000	0.01054	-0.057000	0.13199	-0.710000	0.03640	CAG	.	.	weak		0.547	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382120.2	XM_290540	
TTN	7273	hgsc.bcm.edu	37	2	179427536	179427536	+	Missense_Mutation	SNP	T	T	C	rs3829746	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr2:179427536T>C	ENST00000591111.1	-	276	78624	c.78400A>G	c.(78400-78402)Ata>Gta	p.I26134V	TTN-AS1_ENST00000456053.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.I18710V|TTN-AS1_ENST00000419746.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.I27775V|TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.I25207V|TTN-AS1_ENST00000586831.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.I18835V|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.I18902V|TTN-AS1_ENST00000590807.1_RNA			Q8WZ42	TITIN_HUMAN	titin	26134	Fibronectin type-III 90. {ECO:0000255|PROSITE-ProRule:PRU00316}.		I -> V. {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)			ACTTCTCTTATGGTCAAATTC	0.408													C|||	2546	0.508387	0.5658	0.4078	5008	,	,		21726	0.7153		0.2535	False		,,,				2504	0.5511				p.I27775V		Atlas-SNP	.											.	TTN	18412	.	0			c.A83323G						PASS	.	C	VAL/ILE,VAL/ILE,VAL/ILE,VAL/ILE	2013,1773		546,921,426	64.0	58.0	60.0		56704,56503,75619,56128	5.2	1.0	2	dbSNP_107	60	1841,6417		193,1455,2481	yes	missense,missense,missense,missense	TTN	NM_133437.3,NM_133432.3,NM_133378.4,NM_003319.4	29,29,29,29	739,2376,2907	CC,CT,TT		22.2935,46.8304,31.9993	benign,benign,benign,benign	18902/27119,18835/27052,25207/33424,18710/26927	179427536	3854,8190	1893	4129	6022	SO:0001583	missense	7273	exon326			CTCTTATGGTCAA	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.78400A>G	2.37:g.179427536T>C	ENSP00000465570:p.Ile26134Val	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	119	6	0.0504202	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		980	0.44871794871794873	281	0.5711382113821138	129	0.356353591160221	385	0.6730769230769231	185	0.24406332453825857	C	9.433	1.086053	0.20390	0.531696	0.222935	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.53423	0.62;0.62;0.62;0.62	6.04	5.15	0.70609	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00012	0.0000	N	0.02275	-0.615	0.39703	P	0.028781999999999974	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	0.37314	-0.9711	8	0.87932	D	0	.	9.6301	0.39774	0.0:0.6833:0.0:0.3167	rs3829746;rs11565883;rs56750589;rs3829746	18710;18835;18902;26134	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	V	25207;18710;18902;18835;18708	ENSP00000343764:I25207V;ENSP00000434586:I18710V;ENSP00000340554:I18902V;ENSP00000352154:I18835V	ENSP00000340554:I18902V	I	-	1	0	TTN	179135782	0.155000	0.22806	0.994000	0.49952	0.900000	0.52787	0.683000	0.25349	0.883000	0.36040	-0.215000	0.12644	ATA	T|0.555;C|0.445	0.445	strong		0.408	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
MMP27	64066	hgsc.bcm.edu	37	11	102576382	102576382	+	Missense_Mutation	SNP	G	G	A	rs12099177	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr11:102576382G>A	ENST00000260229.4	-	1	155	c.64C>T	c.(64-66)Cgg>Tgg	p.R22W		NM_022122.2	NP_071405.2	Q9H306	MMP27_HUMAN	matrix metallopeptidase 27	22			R -> W (in dbSNP:rs12099177).		collagen catabolic process (GO:0030574)	proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.R22W(1)		NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(2)|lung(12)|ovary(2)|prostate(2)|skin(11)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	45	all_cancers(8;0.000843)|all_epithelial(12;0.00362)|Lung NSC(15;0.21)	all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)	Epithelial(9;0.0509)|Lung(13;0.0696)|LUSC - Lung squamous cell carcinoma(19;0.13)|all cancers(10;0.176)	BRCA - Breast invasive adenocarcinoma(274;0.0151)	Marimastat(DB00786)	TCCGTCATCCGGACTAAGGGA	0.363													G|||	844	0.16853	0.1687	0.1455	5008	,	,		19020	0.2996		0.0666	False		,,,				2504	0.1544				p.R22W		Atlas-SNP	.											MMP27,NS,carcinoma,0,1	MMP27	84	1	1	Substitution - Missense(1)	stomach(1)	c.C64T						scavenged	.	G	TRP/ARG	741,3665	301.0+/-286.6	67,607,1529	99.0	106.0	104.0		64	0.5	0.0	11	dbSNP_120	104	550,8048	150.4+/-205.3	15,520,3764	yes	missense	MMP27	NM_022122.2	101	82,1127,5293	AA,AG,GG		6.3968,16.818,9.9277	possibly-damaging	22/514	102576382	1291,11713	2203	4299	6502	SO:0001583	missense	64066	exon1			TCATCCGGACTAA	AF195192	CCDS8319.1	11q24	2008-07-18	2005-08-08		ENSG00000137675	ENSG00000137675			14250	protein-coding gene	gene with protein product	"""matrix metalloprotease 27"""		"""matrix metalloproteinase 27"""			10419448	Standard	NM_022122		Approved		uc001phd.1	Q9H306	OTTHUMG00000168099	ENST00000260229.4:c.64C>T	11.37:g.102576382G>A	ENSP00000260229:p.Arg22Trp	Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	193	7	0.0362694	NM_022122	Q6UWK6	Missense_Mutation	SNP	ENST00000260229.4	37	CCDS8319.1	340	0.15567765567765568	93	0.18902439024390244	43	0.11878453038674033	161	0.28146853146853146	43	0.05672823218997362	G	10.72	1.429129	0.25726	0.16818	0.063968	ENSG00000137675	ENST00000260229	T	0.36520	1.25	4.98	0.533	0.17121	.	1.468070	0.05201	U	0.505000	T	0.00012	0.0000	L	0.27053	0.805	0.80722	P	0.0	B	0.21606	0.058	B	0.20384	0.029	T	0.33548	-0.9864	9	0.66056	D	0.02	.	3.9186	0.09234	0.0821:0.1352:0.4882:0.2945	rs12099177;rs60819172;rs12099177	22	Q9H306	MMP27_HUMAN	W	22	ENSP00000260229:R22W	ENSP00000260229:R22W	R	-	1	2	MMP27	102081592	0.002000	0.14202	0.000000	0.03702	0.001000	0.01503	1.091000	0.30915	0.330000	0.23485	0.655000	0.94253	CGG	G|0.882;A|0.118	0.118	strong		0.363	MMP27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398128.1	NM_022122	
WFS1	7466	hgsc.bcm.edu	37	4	6293696	6293696	+	Silent	SNP	C	C	G	rs1801213	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr4:6293696C>G	ENST00000226760.1	+	6	854	c.684C>G	c.(682-684)cgC>cgG	p.R228R	WFS1_ENST00000503569.1_Silent_p.R228R	NM_001145853.1|NM_006005.3	NP_001139325.1|NP_005996.2	O76024	WFS1_HUMAN	Wolfram syndrome 1 (wolframin)	228					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|calcium ion homeostasis (GO:0055074)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER overload response (GO:0006983)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|glucose homeostasis (GO:0042593)|kidney development (GO:0001822)|negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway (GO:1902236)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of programmed cell death (GO:0043069)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of type B pancreatic cell apoptotic process (GO:2000675)|neurological system process (GO:0050877)|olfactory behavior (GO:0042048)|polyubiquitinated misfolded protein transport (GO:0070845)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of growth (GO:0045927)|positive regulation of protein metabolic process (GO:0051247)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of proteolysis (GO:0045862)|protein maturation by protein folding (GO:0022417)|protein stabilization (GO:0050821)|renal water homeostasis (GO:0003091)|response to endoplasmic reticulum stress (GO:0034976)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)	activating transcription factor binding (GO:0033613)|ATPase binding (GO:0051117)|transporter activity (GO:0005215)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(6)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	21				Colorectal(103;0.0512)		AGCAGAGGCGCATGCTGGAGC	0.642													G|||	3788	0.75639	0.6959	0.7378	5008	,	,		16959	0.9038		0.6849	False		,,,				2504	0.773				p.R228R		Atlas-SNP	.											WFS1,NS,carcinoma,0,1	WFS1	71	1	0			c.C684G						scavenged	.	G	,	2938,1454		985,968,243	47.0	40.0	42.0		684,684	1.5	1.0	4	dbSNP_89	42	5870,2728		1999,1872,428	no	coding-synonymous,coding-synonymous	WFS1	NM_001145853.1,NM_006005.3	,	2984,2840,671	GG,GC,CC		31.7283,33.1056,32.194	,	228/891,228/891	6293696	8808,4182	2196	4299	6495	SO:0001819	synonymous_variant	7466	exon6			GAGGCGCATGCTG	AF084481	CCDS3386.1	4p16.1	2014-06-18			ENSG00000109501	ENSG00000109501			12762	protein-coding gene	gene with protein product		606201		DFNA6, DFNA14, DFNA38		7987399, 9771706	Standard	NM_006005		Approved	DIDMOAD, WFS	uc003gix.3	O76024	OTTHUMG00000090431	ENST00000226760.1:c.684C>G	4.37:g.6293696C>G		Somatic	211	0	0		WXS	Illumina HiSeq	Phase_I	199	6	0.0301508	NM_001145853	B2R797|D3DVT1|Q8N6I3|Q9UNW6	Silent	SNP	ENST00000226760.1	37	CCDS3386.1	1662	0.760989010989011	345	0.7012195121951219	266	0.7348066298342542	536	0.9370629370629371	515	0.679419525065963	G	10.35	1.324588	0.24080	0.668944	0.682717	ENSG00000109501	ENST00000506362	.	.	.	4.37	1.53	0.23141	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999124776	.	.	.	.	.	.	T	0.18335	-1.0340	3	.	.	.	-44.9845	6.9398	0.24486	0.2177:0.2494:0.5329:0.0	rs1801213;rs2230718;rs7672995	.	.	.	G	94	.	.	A	+	2	0	WFS1	6344597	0.811000	0.29063	0.994000	0.49952	0.974000	0.67602	-0.097000	0.11042	0.069000	0.16605	-0.216000	0.12614	GCA	C|0.294;G|0.706	0.706	strong		0.642	WFS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206863.1		
REST	5978	hgsc.bcm.edu	37	4	57798189	57798189	+	Silent	SNP	G	G	A	rs2227901	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr4:57798189G>A	ENST00000309042.7	+	4	3479	c.3165G>A	c.(3163-3165)gcG>gcA	p.A1055A		NM_001193508.1|NM_005612.4	NP_001180437.1|NP_005603.3	Q13127	REST_HUMAN	RE1-silencing transcription factor	1055	Interaction with RCOR1.				cardiac muscle cell myoblast differentiation (GO:0060379)|cellular response to drug (GO:0035690)|cellular response to electrical stimulus (GO:0071257)|cellular response to glucocorticoid stimulus (GO:0071385)|hematopoietic progenitor cell differentiation (GO:0002244)|histone H4 deacetylation (GO:0070933)|negative regulation by host of viral transcription (GO:0043922)|negative regulation of aldosterone biosynthetic process (GO:0032348)|negative regulation of amniotic stem cell differentiation (GO:2000798)|negative regulation of calcium ion-dependent exocytosis (GO:0045955)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cortisol biosynthetic process (GO:2000065)|negative regulation of dense core granule biogenesis (GO:2000706)|negative regulation of gene expression (GO:0010629)|negative regulation of insulin secretion (GO:0046676)|negative regulation of mesenchymal stem cell differentiation (GO:2000740)|negative regulation of neurogenesis (GO:0050768)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of transcription, DNA-templated (GO:0045893)|potassium ion transmembrane transport (GO:0071805)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|core promoter binding (GO:0001047)|core promoter sequence-specific DNA binding (GO:0001046)|metal ion binding (GO:0046872)|outward rectifier potassium channel activity (GO:0015271)|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 transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(2)|lung(22)|ovary(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	50	Glioma(25;0.08)|all_neural(26;0.181)					CAGTCAAAGCGGCTAAGGGAG	0.433													G|||	1270	0.253594	0.2595	0.2161	5008	,	,		20278	0.3661		0.1849	False		,,,				2504	0.227				p.A1055A		Atlas-SNP	.											.	REST	104	.	0			c.G3165A						PASS	.	G	,	1041,3365	384.9+/-325.5	111,819,1273	80.0	77.0	78.0		3165,3165	1.1	0.0	4	dbSNP_98	78	1641,6959	303.6+/-306.5	143,1355,2802	no	coding-synonymous,coding-synonymous	REST	NM_001193508.1,NM_005612.4	,	254,2174,4075	AA,AG,GG		19.0814,23.6269,20.6213	,	1055/1098,1055/1098	57798189	2682,10324	2203	4300	6503	SO:0001819	synonymous_variant	5978	exon4			CAAAGCGGCTAAG	U13879	CCDS3509.1	4q12	2008-02-05			ENSG00000084093	ENSG00000084093			9966	protein-coding gene	gene with protein product		600571				7871435, 7697725	Standard	NM_005612		Approved	NRSF, XBR	uc003hci.3	Q13127	OTTHUMG00000128770	ENST00000309042.7:c.3165G>A	4.37:g.57798189G>A		Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	174	11	0.0632184	NM_001193508	A2RUE0|B9EGJ0|Q12956|Q12957|Q13134|Q59ER1|Q8IWI3	Silent	SNP	ENST00000309042.7	37	CCDS3509.1																																																																																			G|0.791;A|0.209	0.209	strong		0.433	REST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250691.2	NM_005612	
MUC4	4585	hgsc.bcm.edu	37	3	195507398	195507398	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr3:195507398C>T	ENST00000463781.3	-	2	11512	c.11053G>A	c.(11053-11055)Gac>Aac	p.D3685N	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.D3685N	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)		GAGGAAGTGTCCGTGACAGGA	0.592																																					p.D3685N		Atlas-SNP	.											MUC4_ENST00000463781,NS,lymphoid_neoplasm,+1,1	MUC4	1505	1	0			c.G11053A						scavenged	.						12.0	12.0	12.0					3																	195507398		561	1429	1990	SO:0001583	missense	4585	exon2			AAGTGTCCGTGAC	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.11053G>A	3.37:g.195507398C>T	ENSP00000417498:p.Asp3685Asn	Somatic	38	4	0.105263		WXS	Illumina HiSeq	Phase_I	52	3	0.0576923	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	8.871	0.949360	0.18356	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.52057	1.16;0.68	0.743	-1.49	0.08718	.	.	.	.	.	T	0.18800	0.0451	N	0.08118	0	0.09310	N	1	P	0.42993	0.797	B	0.34452	0.183	T	0.14952	-1.0454	8	.	.	.	.	5.1792	0.15150	0.0:0.3745:0.6255:0.0	.	3557	E7ESK3	.	N	3685	ENSP00000417498:D3685N;ENSP00000420243:D3685N	.	D	-	1	0	MUC4	196992177	0.000000	0.05858	0.004000	0.12327	0.004000	0.04260	-3.241000	0.00544	0.088000	0.17205	0.089000	0.15464	GAC	.	.	none		0.592	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
PLD2	5338	hgsc.bcm.edu	37	17	4718776	4718776	+	Silent	SNP	G	G	A	rs1132448	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr17:4718776G>A	ENST00000263088.6	+	13	1310	c.1179G>A	c.(1177-1179)gaG>gaA	p.E393E	PLD2_ENST00000572940.1_Silent_p.E393E	NM_001243108.1|NM_002663.4	NP_001230037.1|NP_002654.3	O14939	PLD2_HUMAN	phospholipase D2	393					cytoskeleton organization (GO:0007010)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|G-protein coupled receptor internalization (GO:0002031)|glycerophospholipid biosynthetic process (GO:0046474)|innate immune response (GO:0045087)|lipid catabolic process (GO:0016042)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylglycerol biosynthetic process (GO:0006655)|phospholipid metabolic process (GO:0006644)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	brush border membrane (GO:0031526)|endoplasmic reticulum membrane (GO:0005789)|plasma membrane (GO:0005886)	N-acylphosphatidylethanolamine-specific phospholipase D activity (GO:0070290)|phosphatidylinositol binding (GO:0035091)|phospholipase D activity (GO:0004630)			autonomic_ganglia(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(3)|large_intestine(3)|lung(10)|ovary(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)	31					Choline(DB00122)	ACCAGGAGGAGGGTGTCCGTG	0.542											OREG0024105	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	3131	0.6252	0.388	0.7435	5008	,	,		21414	0.6349		0.7028	False		,,,				2504	0.772				p.E393E		Atlas-SNP	.											.	PLD2	138	.	0			c.G1179A						PASS	.	G		1962,2444	553.3+/-378.7	429,1104,670	311.0	277.0	289.0		1179	2.5	1.0	17	dbSNP_86	289	6193,2407	699.9+/-405.1	2251,1691,358	no	coding-synonymous	PLD2	NM_002663.4		2680,2795,1028	AA,AG,GG		27.9884,44.5302,37.2982		393/934	4718776	8155,4851	2203	4300	6503	SO:0001819	synonymous_variant	5338	exon13			GGAGGAGGGTGTC	AF035483	CCDS11057.1, CCDS58507.1	17p13.3	2008-04-14			ENSG00000129219	ENSG00000129219	3.1.4.4		9068	protein-coding gene	gene with protein product	"""choline phosphatase 2"""	602384				9858823, 9582313	Standard	NM_002663		Approved		uc002fzc.3	O14939	OTTHUMG00000090779	ENST00000263088.6:c.1179G>A	17.37:g.4718776G>A		Somatic	106	0	0	621	WXS	Illumina HiSeq	Phase_I	107	5	0.046729	NM_001243108	I3L2C9|O43540|O43579|O43580|Q6PGR0|Q96BY3	Silent	SNP	ENST00000263088.6	37	CCDS11057.1																																																																																			G|0.370;A|0.630	0.630	strong		0.542	PLD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207561.3	NM_002663	
POTEM	641455	hgsc.bcm.edu	37	14	20010235	20010235	+	Missense_Mutation	SNP	A	A	G	rs113380635		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr14:20010235A>G	ENST00000551509.1	-	5	974	c.923T>C	c.(922-924)gTt>gCt	p.V308A	RP11-244H18.1_ENST00000547584.1_lincRNA|RNU6-1268P_ENST00000391214.1_RNA	NM_001145442.1	NP_001138914.1	A6NI47	POTEM_HUMAN	POTE ankyrin domain family, member M	308										endometrium(4)|kidney(1)|lung(4)	9						AAGTATGAGAACAGTTCTAAA	0.368																																					p.V308A		Atlas-SNP	.											POTEM_ENST00000551509,NS,carcinoma,0,4	POTEM	51	4	0			c.T923C						scavenged	.						42.0	37.0	39.0					14																	20010235		365	763	1128	SO:0001583	missense	641455	exon5			ATGAGAACAGTTC		CCDS73609.1	14q11.2	2013-01-10			ENSG00000187537	ENSG00000187537		"""POTE ankyrin domain containing"", ""Ankyrin repeat domain containing"""	37096	protein-coding gene	gene with protein product	"""prostate-specific P704P"""					16364570	Standard	NM_001145442		Approved	POTE14beta, P704P, ACT	uc001vwc.3	A6NI47		ENST00000551509.1:c.923T>C	14.37:g.20010235A>G	ENSP00000452296:p.Val308Ala	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	72	4	0.0555556	NM_001145442		Missense_Mutation	SNP	ENST00000551509.1	37	CCDS45076.1	.	.	.	.	.	.	.	.	.	.	g	5.617	0.298596	0.10622	.	.	ENSG00000187537	ENST00000551509;ENST00000439503;ENST00000344684	T	0.60040	0.22	0.906	0.906	0.19314	Ankyrin repeat-containing domain (4);	0.000000	0.32655	N	0.005811	T	0.10723	0.0262	N	0.00039	-2.51	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.25187	-1.0139	8	.	.	.	.	3.4158	0.07375	0.2955:0.0:0.7045:0.0	.	308	A6NI47	POTEM_HUMAN	A	308;393;308	ENSP00000452296:V308A	.	V	-	2	0	POTEM	19080235	0.621000	0.27077	0.813000	0.32504	0.042000	0.13812	0.922000	0.28734	-0.020000	0.14032	-1.160000	0.01791	GTT	A|0.250;G|0.750	0.750	weak		0.368	POTEM-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409490.3	NM_001145442	
HAGHL	84264	hgsc.bcm.edu	37	16	778158	778158	+	Silent	SNP	C	C	G	rs1406815	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr16:778158C>G	ENST00000341413.4	+	4	494	c.213C>G	c.(211-213)ccC>ccG	p.P71P	HAGHL_ENST00000564545.1_Missense_Mutation_p.R50G|HAGHL_ENST00000564537.1_Silent_p.P71P|NARFL_ENST00000562862.1_5'Flank|HAGHL_ENST00000549114.1_Silent_p.P71P|CCDC78_ENST00000293889.6_5'Flank|HAGHL_ENST00000561546.1_Silent_p.P71P|HAGHL_ENST00000389703.3_Silent_p.P71P			Q6PII5	HAGHL_HUMAN	hydroxyacylglutathione hydrolase-like	71							hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			lung(3)	3		Hepatocellular(780;0.00335)				GGCTTCGTCCCGGGCTGGCGG	0.781													c|||	2240	0.447284	0.3434	0.4784	5008	,	,		5375	0.7579		0.2396	False		,,,				2504	0.4591				p.P71P	Pancreas(46;538 1326 12403 32360)	Atlas-SNP	.											.	HAGHL	18	.	0			c.C213G						PASS	.						1.0	1.0	1.0					16																	778158		455	1002	1457	SO:0001819	synonymous_variant	84264	exon3			TCGTCCCGGGCTG	AK054841	CCDS32354.1	16p13.3	2008-02-05	2003-11-04						14177	protein-coding gene	gene with protein product			"""hydroxyacyl glutathione hydrolase-like"""			12477932	Standard	XM_005255629		Approved	MGC2605	uc002cjo.1	Q6PII5		ENST00000341413.4:c.213C>G	16.37:g.778158C>G		Somatic	1	0	0		WXS	Illumina HiSeq	Phase_I	8	7	0.875	NM_032304	A6NCC4|D3DU64|Q59FX8|Q96BZ3|Q96NR5|Q96S11|Q9BT45	Silent	SNP	ENST00000341413.4	37																																																																																				C|0.556;G|0.444	0.444	strong		0.781	HAGHL-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000409607.1	NM_032304	
PAEP	5047	hgsc.bcm.edu	37	9	138456155	138456155	+	Missense_Mutation	SNP	C	C	A	rs3748210	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr9:138456155C>A	ENST00000479141.1	+	4	420	c.376C>A	c.(376-378)Cag>Aag	p.Q126K	PAEP_ENST00000277508.5_Missense_Mutation_p.Q126K|PAEP_ENST00000371766.2_Missense_Mutation_p.Q126K	NM_002571.2	NP_002562.2	P09466	PAEP_HUMAN	progestagen-associated endometrial protein	126			Q -> K (in dbSNP:rs3748210).		multicellular organismal development (GO:0007275)|transport (GO:0006810)	extracellular region (GO:0005576)	small molecule binding (GO:0036094)	p.Q126K(1)		cervix(1)|endometrium(1)|lung(1)|prostate(1)|skin(1)|stomach(1)	6				OV - Ovarian serous cystadenocarcinoma(145;3.39e-07)|Epithelial(140;1.11e-06)|all cancers(34;2.04e-05)		TCTCTGCCTACAGGACACCAC	0.547													.|||	1465	0.292532	0.3994	0.2608	5008	,	,		19035	0.497		0.0517	False		,,,				2504	0.2076				p.Q126K		Atlas-SNP	.											PAEP,NS,carcinoma,0,2	PAEP	16	2	1	Substitution - Missense(1)	stomach(1)	c.C376A						PASS	.	A	LYS/GLN,LYS/GLN	1356,2988		203,950,1019	92.0	67.0	76.0		376,376	-0.2	0.0	9	dbSNP_107	76	252,8250		3,246,4002	no	missense,missense	PAEP	NM_001018049.1,NM_002571.2	53,53	206,1196,5021	AA,AC,CC		2.964,31.2155,12.5175	benign,benign	126/181,126/181	138456155	1608,11238	2172	4251	6423	SO:0001583	missense	5047	exon4			TGCCTACAGGACA		CCDS35173.1	9q34	2011-11-15	2008-07-31		ENSG00000122133	ENSG00000122133		"""Lipocalins"""	8573	protein-coding gene	gene with protein product	"""glycodelin-A"", ""glycodelin-S"", ""glycodelin-F"", ""progesterone-associated endometrial protein"", ""glycodelin"", ""PP14 protein (placental protein 14)"", ""pregnancy-associated endometrial alpha-2-globulin"", ""alpha uterine protein"""	173310				3320533, 2016092	Standard	XM_005263405		Approved	PEP, PP14, GdA, GdS, GdF, PAEG, GD, MGC138509, MGC142288	uc004cgd.1	P09466	OTTHUMG00000020914	ENST00000479141.1:c.376C>A	9.37:g.138456155C>A	ENSP00000417898:p.Gln126Lys	Somatic	287	0	0		WXS	Illumina HiSeq	Phase_I	301	14	0.0465116	NM_002571	Q5T6T1|Q9UG92	Missense_Mutation	SNP	ENST00000479141.1	37	CCDS35173.1	601|601	0.2751831501831502|0.2751831501831502	184|184	0.37398373983739835|0.37398373983739835	95|95	0.26243093922651933|0.26243093922651933	280|280	0.48951048951048953|0.48951048951048953	42|42	0.055408970976253295|0.055408970976253295	A|A	1.043|1.043	-0.678353|-0.678353	0.03378|0.03378	0.312155|0.312155	0.02964|0.02964	ENSG00000122133|ENSG00000122133	ENST00000479141;ENST00000371766;ENST00000277508;ENST00000418284|ENST00000454923	T;T;T;T|.	0.05717|.	3.4;3.4;3.4;3.4|.	1.8|1.8	-0.248|-0.248	0.13015|0.13015	Calycin-like (1);Lipocalin/cytosolic fatty-acid binding protein domain (1);Calycin (1);|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.00707|0.00707	-1.245|-1.245	0.80722|0.80722	P|P	0.0|0.0	B;B|.	0.02656|.	0.0;0.0|.	B;B|.	0.01281|.	0.0;0.0|.	T|T	0.43940|0.43940	-0.9360|-0.9360	8|4	0.06494|.	T|.	0.89|.	.|.	2.7485|2.7485	0.05273|0.05273	0.3718:0.2509:0.3773:0.0|0.3718:0.2509:0.3773:0.0	rs3748210;rs60165543|rs3748210;rs60165543	104;126|.	P09466-2;P09466|.	.;PAEP_HUMAN|.	K|K	126;126;126;78|71	ENSP00000417898:Q126K;ENSP00000360831:Q126K;ENSP00000277508:Q126K;ENSP00000401933:Q78K|.	ENSP00000277508:Q126K|.	Q|T	+|+	1|2	0|0	PAEP|PAEP	137595976|137595976	0.001000|0.001000	0.12720|0.12720	0.000000|0.000000	0.03702|0.03702	0.000000|0.000000	0.00434|0.00434	-0.382000|-0.382000	0.07408|0.07408	-0.460000|-0.460000	0.07003|0.07003	-1.346000|-1.346000	0.01242|0.01242	CAG|ACA	.	.	weak		0.547	PAEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055010.1	NM_001018049	
WTAP	9589	hgsc.bcm.edu	37	6	160169258	160169258	+	Silent	SNP	G	G	T	rs7766006	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr6:160169258G>T	ENST00000358372.4	+	6	2066	c.309G>T	c.(307-309)ccG>ccT	p.P103P	SOD2_ENST00000546087.1_Intron|WTAP_ENST00000337387.4_Silent_p.P103P	NM_001270531.1|NM_004906.4	NP_001257460.1|NP_004897.2	Q15007	FL2D_HUMAN	Wilms tumor 1 associated protein	103					cell cycle (GO:0007049)|mRNA methylation (GO:0080009)|mRNA processing (GO:0006397)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)	MIS complex (GO:0036396)|nuclear membrane (GO:0031965)|nuclear speck (GO:0016607)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(6)|prostate(2)|skin(1)|urinary_tract(1)	18		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;1.75e-18)|BRCA - Breast invasive adenocarcinoma(81;5.93e-06)		TCCAGCAGCCGAGCGTTGCCC	0.423													G|||	1304	0.260383	0.1747	0.2161	5008	,	,		20479	0.4256		0.2097	False		,,,				2504	0.2894				p.P103P		Atlas-SNP	.											WTAP,NS,carcinoma,+2,1	WTAP	44	1	0			c.G309T						scavenged	.	G	,,	843,3563	333.3+/-302.9	92,659,1452	63.0	63.0	63.0		309,309,309	2.3	1.0	6	dbSNP_116	63	1498,7102	284.0+/-296.4	138,1222,2940	no	coding-synonymous,coding-synonymous,coding-synonymous	WTAP	NM_004906.3,NM_152857.1,NM_152858.1	,,	230,1881,4392	TT,TG,GG		17.4186,19.133,17.9994	,,	103/397,103/152,103/152	160169258	2341,10665	2203	4300	6503	SO:0001819	synonymous_variant	9589	exon6			GCAGCCGAGCGTT	AJ276706	CCDS5266.1, CCDS5267.1, CCDS75542.1	6q25-q27	2008-02-05			ENSG00000146457	ENSG00000146457			16846	protein-coding gene	gene with protein product		605442				7788527, 11001926	Standard	NM_004906		Approved	KIAA0105, MGC3925	uc003qsl.4	Q15007	OTTHUMG00000015933	ENST00000358372.4:c.309G>T	6.37:g.160169258G>T		Somatic	333	0	0		WXS	Illumina HiSeq	Phase_I	350	5	0.0142857	NM_001270533	Q5TCL8|Q5TCL9|Q96T28|Q9BYJ7|Q9H4E2	Silent	SNP	ENST00000358372.4	37	CCDS5266.1																																																																																			G|0.800;T|0.200	0.200	strong		0.423	WTAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042905.1	NM_152857	
MIS12	79003	hgsc.bcm.edu	37	17	5392791	5392791	+	Silent	SNP	A	A	G	rs74577983	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr17:5392791A>G	ENST00000381165.3	+	3	1162	c.609A>G	c.(607-609)aaA>aaG	p.K203K	DERL2_ENST00000571968.1_5'Flank|MIS12_ENST00000573759.1_Silent_p.K203K	NM_001258217.1|NM_001258219.1|NM_001258220.1|NM_024039.2	NP_001245146.1|NP_001245148.1|NP_001245149.1|NP_076944.1			MIS12 kinetochore complex component											central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|prostate(1)|skin(2)	12						AACGACTGAAAATATCTTAAT	0.383													A|||	189	0.0377396	0.0023	0.0245	5008	,	,		20132	0.0982		0.0189	False		,,,				2504	0.0521				p.K203K		Atlas-SNP	.											.	MIS12	19	.	0			c.A609G						PASS	.	A		22,4380		0,22,2179	53.0	54.0	54.0		609	2.6	0.3	17	dbSNP_132	54	227,8369		1,225,4072	no	coding-synonymous	MIS12	NM_024039.1		1,247,6251	GG,GA,AA		2.6408,0.4998,1.9157		203/206	5392791	249,12749	2201	4298	6499	SO:0001819	synonymous_variant	79003	exon2			ACTGAAAATATCT	AL136906	CCDS11074.1	17p13.3	2013-07-03	2013-07-03		ENSG00000167842	ENSG00000167842			24967	protein-coding gene	gene with protein product		609178	"""MIS12, MIND kinetochore complex component, homolog (yeast)"", ""MIS12, MIND kinetochore complex component, homolog (S. pombe)"""			11230166, 12515822	Standard	NM_001258217		Approved	MGC2488, hMIS12, KNTC2AP, MTW1	uc031qyj.1	Q9H081	OTTHUMG00000102042	ENST00000381165.3:c.609A>G	17.37:g.5392791A>G		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	79	4	0.0506329	NM_001258220		Silent	SNP	ENST00000381165.3	37	CCDS11074.1																																																																																			A|0.972;G|0.028	0.028	strong		0.383	MIS12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219827.1	NM_024039	
RNPS1	10921	hgsc.bcm.edu	37	16	2305693	2305693	+	Silent	SNP	G	G	A	rs117291307	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr16:2305693G>A	ENST00000565678.1	-	7	1256	c.711C>T	c.(709-711)gcC>gcT	p.A237A	RNPS1_ENST00000397086.2_Silent_p.A237A|RNPS1_ENST00000301730.8_Silent_p.A237A|RNPS1_ENST00000566458.1_Silent_p.A214A|RNPS1_ENST00000566397.1_Silent_p.A60A|RNPS1_ENST00000569598.2_Silent_p.A143A|AC009065.1_ENST00000454671.1_Silent_p.T145T|RNPS1_ENST00000568631.1_Silent_p.A237A|RNPS1_ENST00000320225.5_Silent_p.A237A|RNPS1_ENST00000561718.1_Silent_p.A60A|RNPS1_ENST00000567147.1_Intron			Q15287	RNPS1_HUMAN	RNA binding protein S1, serine-rich domain	237	Interaction with SAP18 and ACIN1.|Necessary for interaction with PNN and exon-skipping.|RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|positive regulation of apoptotic process (GO:0043065)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)	ASAP complex (GO:0061574)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	mRNA 3'-UTR binding (GO:0003730)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			endometrium(1)|large_intestine(1)|lung(4)|ovary(2)|urinary_tract(1)	9						GGGCCAGCACGGCGGTGGCAG	0.557													G|||	60	0.0119808	0.0	0.0216	5008	,	,		18398	0.0417		0.002	False		,,,				2504	0.001				p.A237A		Atlas-SNP	.											.	RNPS1	18	.	0			c.C711T						PASS	.	G	,	3,4391	6.2+/-15.9	0,3,2194	27.0	30.0	29.0		711,711	-2.3	1.0	16	dbSNP_132	29	0,8598		0,0,4299	no	coding-synonymous,coding-synonymous	RNPS1	NM_006711.3,NM_080594.2	,	0,3,6493	AA,AG,GG		0.0,0.0683,0.0231	,	237/306,237/306	2305693	3,12989	2197	4299	6496	SO:0001819	synonymous_variant	10921	exon7			CAGCACGGCGGTG	AF015608	CCDS10465.1, CCDS66907.1, CCDS73811.1	16p13.3	2013-02-12	2001-11-28		ENSG00000205937	ENSG00000205937		"""RNA binding motif (RRM) containing"""	10080	protein-coding gene	gene with protein product		606447	"""RNA-binding protein S1, serine-rich domain"""			9580558, 8543184	Standard	XM_005255048		Approved		uc002cpu.3	Q15287	OTTHUMG00000128828	ENST00000565678.1:c.711C>T	16.37:g.2305693G>A		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	167	8	0.0479042	NM_006711	A8K1P0|B4DDU8|B4DZU7|B7ZA17|O75308|Q32P25|Q8WY42|Q9NYG3	Silent	SNP	ENST00000565678.1	37	CCDS10465.1																																																																																			G|0.993;A|0.007	0.007	strong		0.557	RNPS1-007	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435415.1	NM_080594	
OR7G3	390883	hgsc.bcm.edu	37	19	9237436	9237436	+	Missense_Mutation	SNP	G	G	A	rs61745558|rs386806663	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr19:9237436G>A	ENST00000305444.2	-	1	190	c.191C>T	c.(190-192)tCt>tTt	p.S64F		NM_001001958.1	NP_001001958.1	Q8NG95	OR7G3_HUMAN	olfactory receptor, family 7, subfamily G, member 3	64						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(2)|endometrium(1)|large_intestine(3)|liver(1)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	15						GGACAGGATAGAGAGGAGGAA	0.547													G|||	165	0.0329473	0.0946	0.0043	5008	,	,		20641	0.0347		0.002	False		,,,				2504	0.0				p.S64F		Atlas-SNP	.											OR7G3,NS,carcinoma,+1,1	OR7G3	41	1	0			c.C191T						scavenged	.						127.0	101.0	109.0					19																	9237436		2203	4300	6503	SO:0001583	missense	390883	exon1			AGGATAGAGAGGA		CCDS32899.1	19p13.2	2013-09-24			ENSG00000170920	ENSG00000170920		"""GPCR / Class A : Olfactory receptors"""	8467	protein-coding gene	gene with protein product							Standard	NM_001001958		Approved	OST085	uc010xkl.2	Q8NG95	OTTHUMG00000165520	ENST00000305444.2:c.191C>T	19.37:g.9237436G>A	ENSP00000302867:p.Ser64Phe	Somatic	109	2	0.0183486		WXS	Illumina HiSeq	Phase_I	114	4	0.0350877	NM_001001958	Q6IFJ6|Q96R99	Missense_Mutation	SNP	ENST00000305444.2	37	CCDS32899.1	62	0.028388278388278388	41	0.08333333333333333	2	0.0055248618784530384	18	0.03146853146853147	1	0.0013192612137203166	G	5.003	0.186238	0.09495	.	.	ENSG00000170920	ENST00000305444	T	0.01106	5.33	4.02	1.78	0.24846	GPCR, rhodopsin-like superfamily (1);	0.186186	0.26187	U	0.025839	T	0.00144	0.0004	M	0.86805	2.84	0.09310	N	0.999999	P	0.36768	0.569	B	0.36567	0.228	T	0.43861	-0.9365	10	0.72032	D	0.01	.	3.2948	0.06963	0.0937:0.3295:0.4071:0.1697	.	64	Q8NG95	OR7G3_HUMAN	F	64	ENSP00000302867:S64F	ENSP00000302867:S64F	S	-	2	0	OR7G3	9098436	0.000000	0.05858	0.477000	0.27303	0.158000	0.22134	-1.394000	0.02518	0.453000	0.26858	-0.230000	0.12252	TCT	G|0.980;A|0.020	0.020	strong		0.547	OR7G3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384611.1		
DNAH14	127602	hgsc.bcm.edu	37	1	225454386	225454386	+	Missense_Mutation	SNP	T	T	C	rs4653415	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr1:225454386T>C	ENST00000445597.2	+	33	5816	c.5816T>C	c.(5815-5817)aTg>aCg	p.M1939T	DNAH14_ENST00000439375.2_Missense_Mutation_p.M2479T|DNAH14_ENST00000430092.1_Missense_Mutation_p.M2479T			Q0VDD8	DYH14_HUMAN	dynein, axonemal, heavy chain 14	1939					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						GTATCAGATATGTATGGAGCA	0.294													C|||	49	0.00978435	0.0	0.0274	5008	,	,		16501	0.0278		0.0	False		,,,				2504	0.002				p.M2479T		Atlas-SNP	.											.	DNAH14	300	.	0			c.T7436C						PASS	.						119.0	104.0	108.0					1																	225454386		692	1590	2282	SO:0001583	missense	127602	exon49			CAGATATGTATGG	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.5816T>C	1.37:g.225454386T>C	ENSP00000409472:p.Met1939Thr	Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	87	5	0.0574713	NM_001373	A6NG62|A6NNL2|Q0VDD9|Q4VXC7|Q4VXG4|Q4VXG5|Q5VU33|Q5VU34	Missense_Mutation	SNP	ENST00000445597.2	37		37|37	0.01694139194139194|0.01694139194139194	3|3	0.006097560975609756|0.006097560975609756	11|11	0.03038674033149171|0.03038674033149171	23|23	0.04020979020979021|0.04020979020979021	0|0	0.0|0.0	C|C	0.019|0.019	-1.465096|-1.465096	0.01053|0.01053	.|.	.|.	ENSG00000185842|ENSG00000185842	ENST00000450490|ENST00000445597;ENST00000430092;ENST00000439375	.|T;T;T	.|0.40225	.|1.04;1.44;1.44	5.43|5.43	-10.9|-10.9	0.00192|0.00192	.|.	.|.	.|.	.|.	.|.	T|T	0.01489|0.01489	0.0048|0.0048	N|N	0.00661|0.00661	-1.28|-1.28	0.09310|0.09310	N|N	1|1	.|B	.|0.02656	.|0.0	.|B	.|0.01281	.|0.0	T|T	0.04178|0.04178	-1.0971|-1.0971	5|9	.|0.05525	.|T	.|0.97	.|.	2.5508|2.5508	0.04748|0.04748	0.2793:0.3887:0.1468:0.1852|0.2793:0.3887:0.1468:0.1852	rs4653415;rs52791269;rs56465748;rs4653415|rs4653415;rs52791269;rs56465748;rs4653415	.|2479	.|Q0VDD8-4	.|.	R|T	251|1939;2479;2479	.|ENSP00000409472:M1939T;ENSP00000414402:M2479T;ENSP00000392061:M2479T	.|ENSP00000414402:M2479T	C|M	+|+	1|2	0|0	DNAH14|DNAH14	223521009|223521009	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.400000|0.400000	0.30750|0.30750	-2.984000|-2.984000	0.00661|0.00661	-2.255000|-2.255000	0.00696|0.00696	-1.462000|-1.462000	0.01023|0.01023	TGT|ATG	T|0.980;C|0.020	0.020	strong		0.294	DNAH14-007	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000331217.3	XM_059166	
APH1B	83464	hgsc.bcm.edu	37	15	63597857	63597857	+	Missense_Mutation	SNP	T	T	G	rs1047552	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr15:63597857T>G	ENST00000261879.5	+	6	721	c.651T>G	c.(649-651)ttT>ttG	p.F217L	APH1B_ENST00000380343.4_Missense_Mutation_p.F176L|APH1B_ENST00000560716.1_3'UTR	NM_001145646.1|NM_031301.3	NP_001139118.1|NP_112591.2	Q8WW43	APH1B_HUMAN	APH1B gamma secretase subunit	217			F -> L (in dbSNP:rs1047552).		apoptotic signaling pathway (GO:0097190)|membrane protein intracellular domain proteolysis (GO:0031293)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|positive regulation of apoptotic process (GO:0043065)|positive regulation of catalytic activity (GO:0043085)|protein processing (GO:0016485)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|transport vesicle (GO:0030133)	peptidase activity (GO:0008233)	p.F217L(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|stomach(1)|upper_aerodigestive_tract(1)	12						CGTCAGCATTTATAATCCTGG	0.443													T|||	401	0.0800719	0.0575	0.1167	5008	,	,		19199	0.1637		0.0388	False		,,,				2504	0.0409				p.F217L		Atlas-SNP	.											APH1B,NS,carcinoma,0,1	APH1B	27	1	1	Substitution - Missense(1)	stomach(1)	c.T651G	GRCh37	CM086277	APH1B	M	rs1047552	PASS	.	T	LEU/PHE,LEU/PHE	244,4162	141.9+/-177.2	10,224,1969	70.0	74.0	73.0		528,651	0.0	0.0	15	dbSNP_86	73	259,8341	100.8+/-162.1	6,247,4047	yes	missense,missense	APH1B	NM_001145646.1,NM_031301.3	22,22	16,471,6016	GG,GT,TT		3.0116,5.5379,3.8674	benign,benign	176/217,217/258	63597857	503,12503	2203	4300	6503	SO:0001583	missense	83464	exon6			AGCATTTATAATC	AY358698	CCDS10184.1, CCDS45276.1	15q22.2	2013-05-01	2013-05-01		ENSG00000138613	ENSG00000138613			24080	protein-coding gene	gene with protein product		607630	"""anterior pharynx defective 1 homolog B (C. elegans)"""			12110170, 11230166	Standard	NM_031301		Approved	PSFL, APH-1B, DKFZp564D0372	uc002ama.3	Q8WW43	OTTHUMG00000132863	ENST00000261879.5:c.651T>G	15.37:g.63597857T>G	ENSP00000261879:p.Phe217Leu	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	86	5	0.0581395	NM_031301	A8K589|Q564N3|Q6UWQ1|Q9H0S0	Missense_Mutation	SNP	ENST00000261879.5	37	CCDS10184.1	222	0.10164835164835165	43	0.08739837398373984	36	0.09944751381215469	117	0.20454545454545456	26	0.03430079155672823	T	8.914	0.959432	0.18507	0.055379	0.030116	ENSG00000138613	ENST00000380343;ENST00000261879	T;T	0.41065	1.01;1.01	4.93	0.0142	0.14099	.	0.068865	0.64402	D	0.000012	T	0.00039	0.0001	N	0.24115	0.695	0.54753	P	1.799999999996249E-5	B;B	0.20671	0.047;0.047	B;B	0.25506	0.061;0.061	T	0.14896	-1.0456	9	0.45353	T	0.12	-7.5573	7.3785	0.26841	0.0:0.487:0.0:0.513	rs1047552;rs3187561;rs52837075;rs1047552	176;217	Q564N3;Q8WW43	.;APH1B_HUMAN	L	176;217	ENSP00000369700:F176L;ENSP00000261879:F217L	ENSP00000261879:F217L	F	+	3	2	APH1B	61384910	0.121000	0.22262	0.002000	0.10522	0.030000	0.12068	-0.118000	0.10692	-0.029000	0.13827	-0.475000	0.04921	TTT	G|0.065;T|0.935	0.065	strong		0.443	APH1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256337.1	NM_031301	
ITGA5	3678	hgsc.bcm.edu	37	12	54795600	54795600	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr12:54795600C>T	ENST00000293379.4	-	22	2527	c.2266G>A	c.(2266-2268)Gac>Aac	p.D756N	RP11-753H16.3_ENST00000550474.1_RNA|RP11-753H16.5_ENST00000552785.1_RNA	NM_002205.2	NP_002196.2	P08648	ITA5_HUMAN	integrin, alpha 5 (fibronectin receptor, alpha polypeptide)	756					angiogenesis (GO:0001525)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-cell adhesion mediated by integrin (GO:0033631)|cell-substrate adhesion (GO:0031589)|cell-substrate junction assembly (GO:0007044)|endodermal cell differentiation (GO:0035987)|extracellular matrix organization (GO:0030198)|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)|memory (GO:0007613)|negative regulation of anoikis (GO:2000811)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|viral process (GO:0016032)|wound healing, spreading of epidermal cells (GO:0035313)	alphav-beta3 integrin-vitronectin complex (GO:0071062)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|focal adhesion (GO:0005925)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|synapse (GO:0045202)	metal ion binding (GO:0046872)|platelet-derived growth factor receptor binding (GO:0005161)|vascular endothelial growth factor receptor 2 binding (GO:0043184)			NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(11)|ovary(2)|prostate(1)|upper_aerodigestive_tract(2)	34						TTCTTAGTGTCCCGGAGATGA	0.567																																					p.D756N		Atlas-SNP	.											.	ITGA5	99	.	0			c.G2266A						PASS	.						104.0	103.0	104.0					12																	54795600		2203	4300	6503	SO:0001583	missense	3678	exon22			TAGTGTCCCGGAG		CCDS8880.1	12q11-q13	2010-03-23				ENSG00000161638		"""CD molecules"", ""Integrins"""	6141	protein-coding gene	gene with protein product		135620		FNRA		2454952	Standard	NM_002205		Approved	CD49e	uc001sga.3	P08648	OTTHUMG00000169841	ENST00000293379.4:c.2266G>A	12.37:g.54795600C>T	ENSP00000293379:p.Asp756Asn	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	106	42	0.396226	NM_002205	Q96HA5	Missense_Mutation	SNP	ENST00000293379.4	37	CCDS8880.1	.	.	.	.	.	.	.	.	.	.	C	28.3	4.906611	0.92107	.	.	ENSG00000161638	ENST00000293379	T	0.45668	0.89	5.15	5.15	0.70609	Integrin alpha-2 (1);	0.000000	0.85682	D	0.000000	T	0.58119	0.2100	L	0.45581	1.43	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.55477	-0.8135	10	0.44086	T	0.13	.	16.4804	0.84157	0.0:1.0:0.0:0.0	.	756	P08648	ITA5_HUMAN	N	756	ENSP00000293379:D756N	ENSP00000293379:D756N	D	-	1	0	ITGA5	53081867	1.000000	0.71417	0.996000	0.52242	0.998000	0.95712	6.874000	0.75546	2.567000	0.86603	0.655000	0.94253	GAC	.	.	none		0.567	ITGA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406174.1		
IKBKE	9641	hgsc.bcm.edu	37	1	206651107	206651107	+	Silent	SNP	G	G	A	rs2297545	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr1:206651107G>A	ENST00000367120.3	+	8	1090	c.717G>A	c.(715-717)acG>acA	p.T239T	IKBKE_ENST00000537984.1_Silent_p.T154T	NM_001193322.1|NM_014002.3	NP_001180251.1|NP_054721.1	Q14164	IKKE_HUMAN	inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase epsilon	239	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				immune response (GO:0006955)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of type I interferon production (GO:0032480)|NIK/NF-kappaB signaling (GO:0038061)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|protein phosphorylation (GO:0006468)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome membrane (GO:0010008)|nucleus (GO:0005634)|PML body (GO:0016605)	ATP binding (GO:0005524)|IkappaB kinase activity (GO:0008384)|NF-kappaB-inducing kinase activity (GO:0004704)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(6)|lung(13)|ovary(3)|skin(2)	32	Breast(84;0.137)					GGATCACCACGGAGAAGCCGG	0.652													G|||	1580	0.315495	0.1558	0.402	5008	,	,		15713	0.6131		0.2286	False		,,,				2504	0.2526				p.T239T		Atlas-SNP	.											IKBKE,NS,carcinoma,0,1	IKBKE	77	1	0			c.G717A						scavenged	.	G	,,	716,3650		56,604,1523	13.0	14.0	13.0		462,717,717	-9.1	0.1	1	dbSNP_100	13	1791,6755		176,1439,2658	no	coding-synonymous,coding-synonymous,coding-synonymous	IKBKE	NM_001193321.1,NM_001193322.1,NM_014002.3	,,	232,2043,4181	AA,AG,GG		20.9572,16.3995,19.416	,,	154/632,239/658,239/717	206651107	2507,10405	2183	4273	6456	SO:0001819	synonymous_variant	9641	exon8			CACCACGGAGAAG	AB016590	CCDS30996.1, CCDS53464.1, CCDS73019.1	1q31	2014-05-06			ENSG00000143466				14552	protein-coding gene	gene with protein product		605048				10421793, 10882136	Standard	NM_001193321		Approved	IKKE, IKK-i, KIAA0151	uc001hdz.2	Q14164	OTTHUMG00000184613	ENST00000367120.3:c.717G>A	1.37:g.206651107G>A		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	168	4	0.0238095	NM_001193322	D3DT78|Q3B754|Q3KR43|Q5JTS6	Silent	SNP	ENST00000367120.3	37	CCDS30996.1																																																																																			G|0.745;A|0.255	0.255	strong		0.652	IKBKE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088484.1		
ZNF799	90576	hgsc.bcm.edu	37	19	12501852	12501852	+	Missense_Mutation	SNP	C	C	T	rs200077318		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr19:12501852C>T	ENST00000430385.3	-	4	1560	c.1360G>A	c.(1360-1362)Ggg>Agg	p.G454R	CTD-3105H18.14_ENST00000435033.1_Intron|ZNF799_ENST00000419318.1_Missense_Mutation_p.G422R	NM_001080821.2	NP_001074290.1	Q96GE5	ZN799_HUMAN	zinc finger protein 799	454					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)|kidney(2)|large_intestine(4)|lung(4)|ovary(2)|prostate(2)|skin(2)	19						AAGGCTTTCCCACATTTGCAT	0.383																																					p.G454R		Atlas-SNP	.											ZNF799_ENST00000430385,head_neck,carcinoma,0,2	ZNF799	111	2	0			c.G1360A						scavenged	.						75.0	80.0	78.0					19																	12501852		2202	4299	6501	SO:0001583	missense	90576	exon4			CTTTCCCACATTT	BC009517	CCDS45989.1	19p13.2	2013-01-08			ENSG00000196466	ENSG00000196466		"""Zinc fingers, C2H2-type"", ""-"""	28071	protein-coding gene	gene with protein product			"""zinc finger protein 842"""	ZNF842			Standard	NM_001080821		Approved	HIT-40, MGC71805	uc002mts.4	Q96GE5	OTTHUMG00000156408	ENST00000430385.3:c.1360G>A	19.37:g.12501852C>T	ENSP00000411084:p.Gly454Arg	Somatic	155	4	0.0258065		WXS	Illumina HiSeq	Phase_I	143	9	0.0629371	NM_001080821		Missense_Mutation	SNP	ENST00000430385.3	37	CCDS45989.1	.	.	.	.	.	.	.	.	.	.	C	16.12	3.033438	0.54896	.	.	ENSG00000196466	ENST00000419318;ENST00000430385	T;T	0.21361	2.01;2.01	1.31	-1.12	0.09808	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.27349	0.0671	M	0.86097	2.795	0.31959	N	0.608702	B	0.19200	0.034	B	0.28849	0.095	T	0.34179	-0.9839	9	0.72032	D	0.01	.	5.5527	0.17099	0.0:0.6435:0.0:0.3565	.	454	Q96GE5	ZN799_HUMAN	R	422;454	ENSP00000415278:G422R;ENSP00000411084:G454R	ENSP00000415278:G422R	G	-	1	0	ZNF799	12362852	0.004000	0.15560	0.000000	0.03702	0.966000	0.64601	1.363000	0.34159	-0.271000	0.09272	0.430000	0.28490	GGG	.	.	weak		0.383	ZNF799-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344099.2	NM_001080821	
SHISA2	387914	hgsc.bcm.edu	37	13	26620978	26620978	+	Silent	SNP	G	G	T	rs74965018	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr13:26620978G>T	ENST00000319420.3	-	2	616	c.561C>A	c.(559-561)tcC>tcA	p.S187S		NM_001007538.1	NP_001007539.1	Q6UWI4	SHSA2_HUMAN	shisa family member 2	187					multicellular organismal development (GO:0007275)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(7)|ovary(1)|prostate(2)|skin(1)	17						CGCTGGAGCTGGAACTGGCAG	0.632													G|||	648	0.129393	0.1498	0.0663	5008	,	,		18602	0.2351		0.0	False		,,,				2504	0.1708				p.S187S		Atlas-SNP	.											.	SHISA2	43	.	0			c.C561A						PASS	.	G		511,3895	230.1+/-244.4	37,437,1729	63.0	70.0	68.0		561	5.1	1.0	13	dbSNP_131	68	22,8578	16.0+/-53.3	0,22,4278	no	coding-synonymous	SHISA2	NM_001007538.1		37,459,6007	TT,TG,GG		0.2558,11.5978,4.0981		187/296	26620978	533,12473	2203	4300	6503	SO:0001819	synonymous_variant	387914	exon2			GGAGCTGGAACTG		CCDS31951.1	13q12.13	2013-07-31	2013-07-31	2008-04-01	ENSG00000180730	ENSG00000180730		"""Shisa homologs"""	20366	protein-coding gene	gene with protein product			"""chromosome 13 open reading frame 13"", ""transmembrane protein 46"", ""shisa homolog 2 (Xenopus laevis)"""	C13orf13, TMEM46			Standard	NM_001007538		Approved	bA398O19.2, PRO28631, WGAR9166, hShisa	uc001uqm.1	Q6UWI4	OTTHUMG00000016612	ENST00000319420.3:c.561C>A	13.37:g.26620978G>T		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	84	5	0.0595238	NM_001007538	B9EH70|Q5W0G8	Silent	SNP	ENST00000319420.3	37	CCDS31951.1																																																																																			G|0.945;T|0.055	0.055	strong		0.632	SHISA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044239.2	NM_001007538	
MYOM1	8736	hgsc.bcm.edu	37	18	3215158	3215158	+	Missense_Mutation	SNP	C	C	G	rs386800438|rs1791085	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr18:3215158C>G	ENST00000356443.4	-	2	397	c.64G>C	c.(64-66)Gtg>Ctg	p.V22L	MYOM1_ENST00000400569.3_Missense_Mutation_p.V22L|MYOM1_ENST00000261606.7_Missense_Mutation_p.V22L|RP13-270P17.2_ENST00000580139.1_RNA	NM_003803.3|NM_019856.1	NP_003794.3|NP_062830.1	P52179	MYOM1_HUMAN	myomesin 1	22			V -> L (in dbSNP:rs1791085).		muscle contraction (GO:0006936)	M band (GO:0031430)|striated muscle myosin thick filament (GO:0005863)	identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|structural constituent of muscle (GO:0008307)			NS(2)|autonomic_ganglia(1)|central_nervous_system(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(20)|ovary(4)|pancreas(1)|prostate(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	77						GTGCTGCGCACGTCCTTGTTG	0.612													G|||	641	0.127995	0.1339	0.0879	5008	,	,		16535	0.1845		0.0915	False		,,,				2504	0.1278				p.V22L		Atlas-SNP	.											.	MYOM1	192	.	0			c.G64C						PASS	.	G	LEU/VAL,LEU/VAL	501,3711		30,441,1635	56.0	60.0	59.0		64,64	5.7	1.0	18	dbSNP_89	59	729,7753		30,669,3542	yes	missense,missense	MYOM1	NM_003803.3,NM_019856.1	32,32	60,1110,5177	GG,GC,CC		8.5947,11.8946,9.6896	benign,benign	22/1686,22/1590	3215158	1230,11464	2106	4241	6347	SO:0001583	missense	8736	exon2			TGCGCACGTCCTT	AF185573	CCDS45823.1, CCDS45824.1	18p11.31	2014-09-17	2012-10-17		ENSG00000101605	ENSG00000101605		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	7613	protein-coding gene	gene with protein product	"""skelemin"""	603508	"""myomesin 1 (skelemin) (185kD)"", ""myomesin 1 (skelemin) 185kDa"", ""myomesin 1, 185kDa"""			9806852	Standard	NM_019856		Approved		uc002klp.3	P52179	OTTHUMG00000178209	ENST00000356443.4:c.64G>C	18.37:g.3215158C>G	ENSP00000348821:p.Val22Leu	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	101	6	0.0594059	NM_003803	Q14BD6|Q6H969|Q6ZUU0	Missense_Mutation	SNP	ENST00000356443.4	37	CCDS45824.1	253	0.11584249084249085	65	0.13211382113821138	29	0.08011049723756906	91	0.1590909090909091	68	0.08970976253298153	G	2.140	-0.397132	0.04899	0.118946	0.085947	ENSG00000101605	ENST00000356443;ENST00000400569;ENST00000261606	T;T;T	0.37235	1.33;1.33;1.21	5.67	5.67	0.87782	.	0.312462	0.30959	N	0.008527	T	0.00039	0.0001	N	0.01874	-0.695	0.58432	P	6.999999999979245E-6	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.14896	-1.0456	9	0.02654	T	1	.	9.338	0.38062	0.0761:0.1468:0.7771:0.0	rs1791085;rs1791085	22;22	P52179-2;P52179	.;MYOM1_HUMAN	L	22	ENSP00000348821:V22L;ENSP00000383413:V22L;ENSP00000261606:V22L	ENSP00000261606:V22L	V	-	1	0	MYOM1	3205158	1.000000	0.71417	0.984000	0.44739	0.481000	0.33189	2.152000	0.42272	1.414000	0.47017	-0.120000	0.15030	GTG	C|0.887;G|0.113	0.113	strong		0.612	MYOM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441037.2	NM_003803	
RYR1	6261	hgsc.bcm.edu	37	19	39038962	39038962	+	Missense_Mutation	SNP	G	G	T			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr19:39038962G>T	ENST00000359596.3	+	89	12184	c.12184G>T	c.(12184-12186)Gac>Tac	p.D4062Y	RYR1_ENST00000360985.3_Missense_Mutation_p.D4057Y|RYR1_ENST00000355481.4_Missense_Mutation_p.D4057Y			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	4062					calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)	p.D4062Y(1)		NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	CAAGTTCTTCGACATGTTCCT	0.542																																					p.D4062Y		Atlas-SNP	.											RYR1,NS,carcinoma,0,2	RYR1	708	2	1	Substitution - Missense(1)	pancreas(1)	c.G12184T						scavenged	.						182.0	136.0	152.0					19																	39038962		2203	4300	6503	SO:0001583	missense	6261	exon89			TTCTTCGACATGT	J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"""Ion channels / Ryanodine receptors"""	10483	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 137"""	180901	"""central core disease of muscle"""	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.12184G>T	19.37:g.39038962G>T	ENSP00000352608:p.Asp4062Tyr	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	122	3	0.0245902	NM_000540	Q16314|Q16368|Q9NPK1|Q9P1U4	Missense_Mutation	SNP	ENST00000359596.3	37	CCDS33011.1	.	.	.	.	.	.	.	.	.	.	G	14.46	2.542795	0.45280	.	.	ENSG00000196218	ENST00000359596;ENST00000355481;ENST00000360985	T;T;T	0.68903	-0.36;-0.36;-0.36	4.36	4.36	0.52297	.	0.000000	0.64402	U	0.000001	D	0.83464	0.5260	M	0.84511	2.7	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.998	D	0.86817	0.2002	10	0.87932	D	0	.	17.0495	0.86514	0.0:0.0:1.0:0.0	.	4057;4057;4062	P21817-3;P21817-2;P21817	.;.;RYR1_HUMAN	Y	4062;4057;4057	ENSP00000352608:D4062Y;ENSP00000347667:D4057Y;ENSP00000354254:D4057Y	ENSP00000347667:D4057Y	D	+	1	0	RYR1	43730802	1.000000	0.71417	0.989000	0.46669	0.975000	0.68041	9.520000	0.98027	2.441000	0.82636	0.561000	0.74099	GAC	.	.	none		0.542	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1		
PLGLB1	5343	hgsc.bcm.edu	37	2	87244699	87244699	+	Silent	SNP	T	T	C			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr2:87244699T>C	ENST00000355705.3	-	2	230	c.162A>G	c.(160-162)gaA>gaG	p.E54E	PLGLB1_ENST00000478636.1_5'UTR|PLGLB1_ENST00000409310.2_Silent_p.E54E	NM_001032392.2	NP_001027564.1	Q02325	PLGB_HUMAN	plasminogen-like B1	54	PAN. {ECO:0000255|PROSITE- ProRule:PRU00315}.					extracellular region (GO:0005576)		p.E54E(1)		large_intestine(1)	1						CTTTGTCCTCTTCACATTTTG	0.443																																					p.E54E		Atlas-SNP	.											PLGLB1,rectum,carcinoma,0,1	PLGLB2	1	1	1	Substitution - coding silent(1)	large_intestine(1)	c.A162G						scavenged	.						1.0	1.0	1.0					2																	87244699		69	171	240	SO:0001819	synonymous_variant	5342	exon2			GTCCTCTTCACAT	M86874, M86875, M86876	CCDS33238.1	2p11.2	2008-02-05	2005-03-31	2005-03-31	ENSG00000183281	ENSG00000183281			9072	protein-coding gene	gene with protein product		173340	"""plasminogen-like"""	PLGL		1554698, 2714803	Standard	NM_001032392		Approved	PRP-B		Q02325	OTTHUMG00000154612	ENST00000355705.3:c.162A>G	2.37:g.87244699T>C		Somatic	1219	0	0		WXS	Illumina HiSeq	Phase_I	1123	3	0.00267142	NM_002665	Q580R1	Silent	SNP	ENST00000355705.3	37	CCDS33238.1																																																																																			.	.	none		0.443	PLGLB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330379.1		
WRNIP1	56897	hgsc.bcm.edu	37	6	2784571	2784571	+	Silent	SNP	G	G	A	rs160703	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr6:2784571G>A	ENST00000380773.4	+	6	1865	c.1656G>A	c.(1654-1656)ccG>ccA	p.P552P	WRNIP1_ENST00000380764.1_Silent_p.P168P|WRNIP1_ENST00000380771.4_Silent_p.P527P|WRNIP1_ENST00000380769.4_Silent_p.P332P	NM_020135.2	NP_064520.2			Werner helicase interacting protein 1											breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(1)|lung(2)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	14	Ovarian(93;0.0412)	all_hematologic(90;0.0895)				TGGCAGACCCGTCTGCGTTAA	0.502													G|||	1052	0.210064	0.0968	0.2147	5008	,	,		20281	0.256		0.1968	False		,,,				2504	0.3262				p.P552P		Atlas-SNP	.											.	WRNIP1	39	.	0			c.G1656A						PASS	.	G	,	464,3942	219.1+/-236.9	32,400,1771	113.0	88.0	96.0		1656,1581	-11.1	0.1	6	dbSNP_79	96	1689,6911	308.8+/-309.1	169,1351,2780	no	coding-synonymous,coding-synonymous	WRNIP1	NM_020135.2,NM_130395.1	,	201,1751,4551	AA,AG,GG		19.6395,10.5311,16.5539	,	552/666,527/641	2784571	2153,10853	2203	4300	6503	SO:0001819	synonymous_variant	56897	exon6			AGACCCGTCTGCG	AB056152	CCDS4475.1, CCDS4476.1	6p25.2	2010-04-21			ENSG00000124535	ENSG00000124535		"""ATPases / AAA-type"""	20876	protein-coding gene	gene with protein product		608196				11301316	Standard	NM_020135		Approved	WHIP, FLJ22526, bA420G6.2	uc003mtz.3	Q96S55	OTTHUMG00000014126	ENST00000380773.4:c.1656G>A	6.37:g.2784571G>A		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	65	4	0.0615385	NM_020135		Silent	SNP	ENST00000380773.4	37	CCDS4475.1																																																																																			G|0.824;A|0.176	0.176	strong		0.502	WRNIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039641.1	NM_130395	
LAMA2	3908	hgsc.bcm.edu	37	6	129511373	129511373	+	Silent	SNP	T	T	C	rs2306220	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr6:129511373T>C	ENST00000421865.2	+	11	1540	c.1491T>C	c.(1489-1491)tgT>tgC	p.C497C		NM_000426.3|NM_001079823.1	NP_000417|NP_001073291.1	P24043	LAMA2_HUMAN	laminin, alpha 2	497	Laminin EGF-like 4. {ECO:0000255|PROSITE- ProRule:PRU00460}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|myelination in peripheral nervous system (GO:0022011)|positive regulation of synaptic transmission, cholinergic (GO:0032224)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|sarcolemma (GO:0042383)	structural molecule activity (GO:0005198)			NS(2)|biliary_tract(2)|breast(10)|central_nervous_system(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(35)|lung(84)|ovary(10)|prostate(4)|skin(9)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(2)	194				OV - Ovarian serous cystadenocarcinoma(136;0.178)|all cancers(137;0.245)		GAGGAGACTGTAGTCGTTGCA	0.418													T|||	283	0.0565096	0.0166	0.013	5008	,	,		19927	0.1339		0.0189	False		,,,				2504	0.1002				p.C497C		Atlas-SNP	.											.	LAMA2	481	.	0			c.T1491C						PASS	.	T	,	60,4346	58.7+/-95.3	0,60,2143	135.0	132.0	133.0		1491,1491	0.6	1.0	6	dbSNP_100	133	96,8504	53.1+/-113.8	1,94,4205	no	coding-synonymous,coding-synonymous	LAMA2	NM_000426.3,NM_001079823.1	,	1,154,6348	CC,CT,TT		1.1163,1.3618,1.1994	,	497/3123,497/3119	129511373	156,12850	2203	4300	6503	SO:0001819	synonymous_variant	3908	exon11			AGACTGTAGTCGT	Z26653	CCDS5138.1	6q22-q23	2014-09-17	2008-08-01		ENSG00000196569	ENSG00000196569		"""Laminins"""	6482	protein-coding gene	gene with protein product	"""merosin"", ""congenital muscular dystrophy"""	156225		LAMM		2185464, 8294519	Standard	NM_000426		Approved		uc003qbn.3	P24043	OTTHUMG00000015545	ENST00000421865.2:c.1491T>C	6.37:g.129511373T>C		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	55	4	0.0727273	NM_000426	Q14736|Q5VUM2|Q93022	Silent	SNP	ENST00000421865.2	37	CCDS5138.1																																																																																			T|0.969;C|0.031	0.031	strong		0.418	LAMA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042180.1		
SEMA6D	80031	hgsc.bcm.edu	37	15	48063076	48063076	+	Silent	SNP	T	T	C	rs568215	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr15:48063076T>C	ENST00000316364.5	+	19	2755	c.2316T>C	c.(2314-2316)ccT>ccC	p.P772P	SEMA6D_ENST00000558816.1_3'UTR|SEMA6D_ENST00000536845.2_Silent_p.P772P|SEMA6D_ENST00000389433.2_Silent_p.P753P|SEMA6D_ENST00000355997.3_3'UTR|SEMA6D_ENST00000354744.4_Silent_p.P716P|SEMA6D_ENST00000537942.1_Silent_p.P710P|SEMA6D_ENST00000389428.3_Silent_p.P697P|SEMA6D_ENST00000358066.4_Silent_p.P710P|SEMA6D_ENST00000558014.1_Silent_p.P710P|SEMA6D_ENST00000389432.2_Silent_p.P729P	NM_153618.1	NP_705871.1	Q8NFY4	SEM6D_HUMAN	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D	772					axon guidance (GO:0007411)|negative regulation of smooth muscle cell migration (GO:0014912)|positive regulation of smooth muscle cell migration (GO:0014911)|ventricular system development (GO:0021591)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			biliary_tract(1)|breast(4)|endometrium(4)|kidney(5)|large_intestine(10)|lung(42)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(4)	77		all_lung(180;0.000635)|Myeloproliferative disorder(241;0.116)|Melanoma(134;0.18)		all cancers(107;1.2e-11)|GBM - Glioblastoma multiforme(94;1.2e-06)		CTGCTCTTCCTACTCCTGAGT	0.527													C|||	3985	0.795727	0.9811	0.6527	5008	,	,		17316	0.8442		0.6352	False		,,,				2504	0.7618				p.P772P		Atlas-SNP	.											.	SEMA6D	322	.	0			c.T2316C						PASS	.	C	,,,,,	4037,357	169.8+/-200.3	1859,319,19	59.0	61.0	60.0		2130,2130,2091,2148,2316,	-1.1	1.0	15	dbSNP_83	60	5223,3371	484.6+/-371.4	1598,2027,672	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,utr-3	SEMA6D	NM_001198999.1,NM_020858.1,NM_153616.1,NM_153617.1,NM_153618.1,NM_153619.1	,,,,,	3457,2346,691	CC,CT,TT		39.225,8.1247,28.7034	,,,,,	710/1012,710/1012,697/999,716/1018,772/1074,	48063076	9260,3728	2197	4297	6494	SO:0001819	synonymous_variant	80031	exon19			TCTTCCTACTCCT	AF389430	CCDS32224.1, CCDS32225.1, CCDS32226.1, CCDS32227.1, CCDS32228.1, CCDS32229.1	15q21.1	2006-09-18				ENSG00000137872		"""Semaphorins"""	16770	protein-coding gene	gene with protein product		609295				12110693, 14977921	Standard	NM_020858		Approved	KIAA1479, FLJ11598	uc001zvy.3	Q8NFY4		ENST00000316364.5:c.2316T>C	15.37:g.48063076T>C		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	107	6	0.0560748	NM_153618	A6NF10|A6NM95|A6NNK1|A7E2A0|Q8NFY3|Q8NFY5|Q8NFY6|Q8NFY7|Q9P249	Silent	SNP	ENST00000316364.5	37	CCDS32225.1																																																																																			T|0.258;C|0.742	0.742	strong		0.527	SEMA6D-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416868.1	NM_024966	
NBN	4683	hgsc.bcm.edu	37	8	90958422	90958422	+	Silent	SNP	T	T	C	rs1061302	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr8:90958422T>C	ENST00000265433.3	-	13	2170	c.2016A>G	c.(2014-2016)ccA>ccG	p.P672P	NBN_ENST00000409330.1_Silent_p.P590P	NM_002485.4	NP_002476.2	O60934	NBN_HUMAN	nibrin	672					blastocyst growth (GO:0001832)|cell cycle arrest (GO:0007050)|cell proliferation (GO:0008283)|DNA damage checkpoint (GO:0000077)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA duplex unwinding (GO:0032508)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|intrinsic apoptotic signaling pathway (GO:0097193)|isotype switching (GO:0045190)|meiotic nuclear division (GO:0007126)|mitotic cell cycle checkpoint (GO:0007093)|mitotic G2 DNA damage checkpoint (GO:0007095)|neuromuscular process controlling balance (GO:0050885)|positive regulation of kinase activity (GO:0033674)|positive regulation of protein autophosphorylation (GO:0031954)|regulation of DNA-dependent DNA replication initiation (GO:0030174)|telomere maintenance (GO:0000723)	Mre11 complex (GO:0030870)|nuclear chromosome, telomeric region (GO:0000784)|nuclear inclusion body (GO:0042405)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|replication fork (GO:0005657)|site of double-strand break (GO:0035861)	damaged DNA binding (GO:0003684)|protein N-terminus binding (GO:0047485)|transcription factor binding (GO:0008134)			autonomic_ganglia(1)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(2)|lung(7)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	27			BRCA - Breast invasive adenocarcinoma(11;0.0344)			TTATGCCAGATGGATTTCTGG	0.323								Homologous recombination					T|||	1767	0.352835	0.2156	0.3761	5008	,	,		16654	0.4673		0.3062	False		,,,				2504	0.4519				p.P672P		Atlas-SNP	.											.	NBN	86	.	0			c.A2016G						PASS	.	T		1003,3403	371.2+/-319.9	121,761,1321	107.0	108.0	108.0		2016	-7.3	0.0	8	dbSNP_86	108	2692,5904	430.6+/-356.6	410,1872,2016	no	coding-synonymous	NBN	NM_002485.4		531,2633,3337	CC,CT,TT		31.3169,22.7644,28.4187		672/755	90958422	3695,9307	2203	4298	6501	SO:0001819	synonymous_variant	4683	exon13			GCCAGATGGATTT	AF058696	CCDS6249.1	8q21-q24	2014-09-17	2005-06-02	2005-06-02	ENSG00000104320	ENSG00000104320			7652	protein-coding gene	gene with protein product		602667	"""Nijmegen breakage syndrome 1 (nibrin)"""	NBS, NBS1		9590181, 9590180	Standard	XM_005250923		Approved	ATV, AT-V2, AT-V1	uc003yej.1	O60934	OTTHUMG00000153546	ENST00000265433.3:c.2016A>G	8.37:g.90958422T>C		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	115	8	0.0695652	NM_002485	B2R626|B2RNC5|O60672|Q32NF7|Q53FM6|Q63HR6|Q7LDM2	Silent	SNP	ENST00000265433.3	37	CCDS6249.1																																																																																			T|0.690;C|0.310	0.310	strong		0.323	NBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331583.3	NM_001024688	
GALNTL5	168391	hgsc.bcm.edu	37	7	151668119	151668119	+	Missense_Mutation	SNP	G	G	A	rs181262306	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr7:151668119G>A	ENST00000392800.2	+	3	591	c.337G>A	c.(337-339)Gaa>Aaa	p.E113K	GALNTL5_ENST00000431418.2_Missense_Mutation_p.E113K	NM_145292.3	NP_660335.2	Q7Z4T8	GLTL5_HUMAN	polypeptide N-acetylgalactosaminyltransferase-like 5	113					spermatid development (GO:0007286)	endosome (GO:0005768)|integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)	p.E113K(1)		NS(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(11)|ovary(2)|prostate(2)|skin(3)	32	all_neural(206;0.187)	all_hematologic(28;0.0749)	OV - Ovarian serous cystadenocarcinoma(82;0.00427)	UCEC - Uterine corpus endometrioid carcinoma (81;0.18)|BRCA - Breast invasive adenocarcinoma(188;0.166)		CTTGGGCATCGAAAGAGAAGT	0.333													G|||	7	0.00139776	0.0	0.0014	5008	,	,		16015	0.006		0.0	False		,,,				2504	0.0				p.E113K		Atlas-SNP	.											GALNTL5,scalp,carcinoma,0,2	GALNTL5	87	2	1	Substitution - Missense(1)	skin(1)	c.G337A						scavenged	.						81.0	83.0	82.0					7																	151668119		2203	4299	6502	SO:0001583	missense	168391	exon3			GGCATCGAAAGAG	AF440400	CCDS5929.1	7q36.2	2014-03-13	2014-03-13	2004-07-28	ENSG00000106648	ENSG00000106648		"""Glycosyltransferase family 2 domain containing"""	21725	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase-like 5"""	615133	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 15"", ""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase-like 5"""	GALNT15			Standard	NM_145292		Approved	GalNAc-T5L	uc003wkp.3	Q7Z4T8	OTTHUMG00000157306	ENST00000392800.2:c.337G>A	7.37:g.151668119G>A	ENSP00000376548:p.Glu113Lys	Somatic	261	2	0.00766284		WXS	Illumina HiSeq	Phase_I	291	4	0.0137457	NM_145292	Q75KN2|Q75MD3|Q8NCV4|Q8WW05|Q9UDR9	Missense_Mutation	SNP	ENST00000392800.2	37	CCDS5929.1	5	0.0022893772893772895	0	0.0	1	0.0027624309392265192	4	0.006993006993006993	0	0.0	G	11.48	1.650940	0.29336	.	.	ENSG00000106648	ENST00000431418;ENST00000392800	T;T	0.58940	0.3;0.3	4.94	-9.88	0.00467	.	1.940980	0.02254	N	0.066866	T	0.35128	0.0921	L	0.42245	1.32	0.09310	N	1	B	0.18166	0.026	B	0.08055	0.003	T	0.31447	-0.9943	10	0.66056	D	0.02	.	6.3267	0.21246	0.2813:0.513:0.113:0.0926	.	113	Q7Z4T8	GLTL5_HUMAN	K	113	ENSP00000392582:E113K;ENSP00000376548:E113K	ENSP00000376548:E113K	E	+	1	0	GALNTL5	151299052	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.547000	0.02186	-2.404000	0.00576	-0.882000	0.02950	GAA	G|0.998;A|0.002	0.002	strong		0.333	GALNTL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348395.1	NM_145292	
ALPK2	115701	hgsc.bcm.edu	37	18	56204489	56204489	+	Missense_Mutation	SNP	C	C	G	rs3809975	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr18:56204489C>G	ENST00000361673.3	-	5	3143	c.2930G>C	c.(2929-2931)aGt>aCt	p.S977T	RP11-1151B14.4_ENST00000591360.1_RNA	NM_052947.3	NP_443179.3	Q86TB3	ALPK2_HUMAN	alpha-kinase 2	977			S -> T (in dbSNP:rs3809975).			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						TGAACTATAACTGGCTGGTGT	0.463													C|||	302	0.0603035	0.0053	0.1441	5008	,	,		23148	0.119		0.0318	False		,,,				2504	0.044				p.S977T		Atlas-SNP	.											.	ALPK2	487	.	0			c.G2930C						PASS	.	C	THR/SER	32,4374	37.6+/-69.7	0,32,2171	98.0	96.0	96.0		2930	0.2	0.0	18	dbSNP_107	96	260,8340	101.2+/-162.5	6,248,4046	yes	missense	ALPK2	NM_052947.3	58	6,280,6217	GG,GC,CC		3.0233,0.7263,2.2451	probably-damaging	977/2171	56204489	292,12714	2203	4300	6503	SO:0001583	missense	115701	exon5			CTATAACTGGCTG	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.2930G>C	18.37:g.56204489C>G	ENSP00000354991:p.Ser977Thr	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	118	6	0.0508475	NM_052947	Q6ZUX0|Q8NAT5|Q96L95	Missense_Mutation	SNP	ENST00000361673.3	37	CCDS11966.2	141	0.06456043956043957	8	0.016260162601626018	43	0.11878453038674033	66	0.11538461538461539	24	0.0316622691292876	C	11.05	1.525298	0.27299	0.007263	0.030233	ENSG00000198796	ENST00000361673	T	0.50548	0.74	5.57	0.184	0.15086	.	2.504700	0.01033	N	0.004167	T	0.00580	0.0019	L	0.42245	1.32	0.80722	P	0.0	B;B	0.16396	0.013;0.017	B;B	0.18263	0.021;0.014	T	0.06215	-1.0839	9	0.38643	T	0.18	-0.0959	2.0327	0.03533	0.2207:0.491:0.1303:0.158	rs3809975;rs52789250;rs3809975	977;977	Q86TB3-2;Q86TB3	.;ALPK2_HUMAN	T	977	ENSP00000354991:S977T	ENSP00000354991:S977T	S	-	2	0	ALPK2	54355469	0.000000	0.05858	0.001000	0.08648	0.004000	0.04260	-0.759000	0.04761	0.315000	0.23110	0.591000	0.81541	AGT	C|0.962;G|0.038	0.038	strong		0.463	ALPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256126.1	NM_052947	
UNC13C	440279	hgsc.bcm.edu	37	15	54847677	54847677	+	Silent	SNP	C	C	T	rs11639005	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr15:54847677C>T	ENST00000260323.11	+	28	5925	c.5925C>T	c.(5923-5925)tgC>tgT	p.C1975C	UNC13C_ENST00000545554.1_Silent_p.C1975C|UNC13C_ENST00000537900.1_Silent_p.C1973C	NM_001080534.1	NP_001074003.1	Q8NB66	UN13C_HUMAN	unc-13 homolog C (C. elegans)	1975	MHD2. {ECO:0000255|PROSITE- ProRule:PRU00588}.				exocytosis (GO:0006887)|intracellular signal transduction (GO:0035556)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)			breast(3)|endometrium(5)|kidney(5)|large_intestine(20)|lung(70)|ovary(6)|pancreas(2)|prostate(2)|upper_aerodigestive_tract(4)|urinary_tract(4)	121				GBM - Glioblastoma multiforme(80;0.0789)|all cancers(107;0.124)		CAAGACAATGCGCTATAATGG	0.453													C|||	2050	0.409345	0.1233	0.464	5008	,	,		18348	0.5427		0.4423	False		,,,				2504	0.5859				p.C1975C		Atlas-SNP	.											.	UNC13C	674	.	0			c.C5925T						PASS	.	C		680,3214		57,566,1324	80.0	77.0	78.0		5925	-4.4	0.0	15	dbSNP_120	78	3562,4696		787,1988,1354	no	coding-synonymous	UNC13C	NM_001080534.1		844,2554,2678	TT,TC,CC		43.1339,17.4628,34.9078		1975/2215	54847677	4242,7910	1947	4129	6076	SO:0001819	synonymous_variant	440279	exon27			ACAATGCGCTATA	AK091491	CCDS45264.1	15q21.3	2012-10-02			ENSG00000137766	ENSG00000137766			23149	protein-coding gene	gene with protein product		614568					Standard	NM_001080534		Approved	Munc13-3, DKFZp547H074	uc021smr.1	Q8NB66	OTTHUMG00000172542	ENST00000260323.11:c.5925C>T	15.37:g.54847677C>T		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	95	7	0.0736842	NM_001080534	Q0P613|Q8ND48|Q96NP3	Silent	SNP	ENST00000260323.11	37	CCDS45264.1																																																																																			C|0.625;T|0.375	0.375	strong		0.453	UNC13C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000419028.3	NM_173166	
ZNF354A	6940	hgsc.bcm.edu	37	5	178154018	178154018	+	Missense_Mutation	SNP	T	T	C	rs146060491		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr5:178154018T>C	ENST00000335815.2	-	3	339	c.142A>G	c.(142-144)Agg>Ggg	p.R48G		NM_005649.2	NP_005640.2	O60765	Z354A_HUMAN	zinc finger protein 354A	48	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|sensory perception of sound (GO:0007605)|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)|large_intestine(7)|lung(3)|ovary(2)|skin(2)|stomach(2)	19	all_cancers(89;0.000536)|Renal(175;0.000159)|all_epithelial(37;0.000221)|Lung NSC(126;0.00308)|all_lung(126;0.00536)	all_cancers(40;0.0452)|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)	all cancers(165;0.185)		ACCAGGTTCCTATAGTTCTCC	0.473																																					p.R48G		Atlas-SNP	.											ZNF354A,NS,carcinoma,+1,1	ZNF354A	74	1	0			c.A142G						PASS	.	T	GLY/ARG	1,4405	2.1+/-5.4	0,1,2202	106.0	106.0	106.0		142	2.4	0.0	5	dbSNP_134	106	0,8600		0,0,4300	no	missense	ZNF354A	NM_005649.2	125	0,1,6502	CC,CT,TT		0.0,0.0227,0.0077	benign	48/606	178154018	1,13005	2203	4300	6503	SO:0001583	missense	6940	exon3			GGTTCCTATAGTT	AF116030	CCDS4438.1	5q35.3	2013-01-08		2001-11-23	ENSG00000169131	ENSG00000169131		"""Zinc fingers, C2H2-type"", ""-"""	11628	protein-coding gene	gene with protein product		602444		TCF17		9465904	Standard	NM_005649		Approved	KID-1, EZNF, HKL1, KID1	uc003mjj.3	O60765	OTTHUMG00000130895	ENST00000335815.2:c.142A>G	5.37:g.178154018T>C	ENSP00000337122:p.Arg48Gly	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	107	5	0.046729	NM_005649	Q9UNJ8	Missense_Mutation	SNP	ENST00000335815.2	37	CCDS4438.1	.	.	.	.	.	.	.	.	.	.	T	0.012	-1.676225	0.00751	2.27E-4	0.0	ENSG00000169131	ENST00000335815;ENST00000520331	T;T	0.01981	4.52;4.52	3.63	2.44	0.29823	Krueppel-associated box (4);	.	.	.	.	T	0.01695	0.0054	N	0.20483	0.58	0.09310	N	1	B	0.12013	0.005	B	0.16722	0.016	T	0.47761	-0.9092	9	0.36615	T	0.2	-0.5793	3.9416	0.09329	0.0:0.1171:0.215:0.6679	.	48	O60765	Z354A_HUMAN	G	48	ENSP00000337122:R48G;ENSP00000429675:R48G	ENSP00000337122:R48G	R	-	1	2	ZNF354A	178086624	0.000000	0.05858	0.002000	0.10522	0.068000	0.16541	0.135000	0.15952	0.569000	0.29329	0.459000	0.35465	AGG	T|1.000;C|0.000	0.000	weak		0.473	ZNF354A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253481.1	NM_005649	
OR7A10	390892	hgsc.bcm.edu	37	19	14951929	14951929	+	Missense_Mutation	SNP	G	G	T			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr19:14951929G>T	ENST00000248058.1	-	1	760	c.761C>A	c.(760-762)aCa>aAa	p.T254K		NM_001005190.1	NP_001005190.1	O76100	OR7AA_HUMAN	olfactory receptor, family 7, subfamily A, member 10	254						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)|kidney(2)|large_intestine(4)|lung(9)|stomach(1)	19	Ovarian(108;0.203)					CCCTAAGCATGTACCATAAAA	0.493																																					p.T254K		Atlas-SNP	.											OR7A10,NS,carcinoma,-1,1	OR7A10	33	1	0			c.C761A						PASS	.						103.0	88.0	93.0					19																	14951929		2203	4300	6503	SO:0001583	missense	390892	exon1			AAGCATGTACCAT		CCDS32936.1	19p13.1	2012-08-09						"""GPCR / Class A : Olfactory receptors"""	8356	protein-coding gene	gene with protein product							Standard	NM_001005190		Approved		uc002mzx.1	O76100		ENST00000248058.1:c.761C>A	19.37:g.14951929G>T	ENSP00000248058:p.Thr254Lys	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	92	30	0.326087	NM_001005190	Q6IFP0|Q96R97	Missense_Mutation	SNP	ENST00000248058.1	37	CCDS32936.1	.	.	.	.	.	.	.	.	.	.	g	14.39	2.519896	0.44866	.	.	ENSG00000127515	ENST00000248058	T	0.00287	8.29	2.75	1.65	0.23941	GPCR, rhodopsin-like superfamily (1);	0.000000	0.40144	U	0.001177	T	0.01092	0.0036	H	0.98754	4.32	0.09310	N	1	D	0.64830	0.994	D	0.68943	0.961	T	0.24657	-1.0154	10	0.87932	D	0	.	9.5406	0.39248	0.0:0.2179:0.7821:0.0	.	254	O76100	OR7AA_HUMAN	K	254	ENSP00000248058:T254K	ENSP00000248058:T254K	T	-	2	0	OR7A10	14812929	0.008000	0.16893	0.001000	0.08648	0.236000	0.25371	1.536000	0.36072	0.499000	0.27970	0.134000	0.15878	ACA	.	.	none		0.493	OR7A10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466520.1	NM_001005190	
MAP3K5	4217	hgsc.bcm.edu	37	6	136977568	136977568	+	Silent	SNP	T	T	C	rs2076260	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr6:136977568T>C	ENST00000359015.4	-	10	1917	c.1557A>G	c.(1555-1557)ttA>ttG	p.L519L	MAP3K5_ENST00000355845.4_5'UTR	NM_005923.3	NP_005914.1	Q99683	M3K5_HUMAN	mitogen-activated protein kinase kinase kinase 5	519					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of JUN kinase activity (GO:0007257)|activation of MAPKK activity (GO:0000186)|apoptotic signaling pathway (GO:0097190)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to reactive nitrogen species (GO:1902170)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|JNK cascade (GO:0007254)|MAPK cascade (GO:0000165)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of neuron death (GO:1901216)|programmed necrotic cell death (GO:0097300)|protein phosphorylation (GO:0006468)|response to ischemia (GO:0002931)|viral process (GO:0016032)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|protein kinase complex (GO:1902911)	ATP binding (GO:0005524)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|magnesium ion binding (GO:0000287)|MAP kinase kinase kinase activity (GO:0004709)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein phosphatase binding (GO:0019903)			NS(1)|breast(1)|cervix(1)|endometrium(8)|kidney(6)|large_intestine(6)|lung(24)|ovary(2)|prostate(1)|skin(4)|urinary_tract(4)	58	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00137)|OV - Ovarian serous cystadenocarcinoma(155;0.00569)		GCTTATATATTAAAATTGTCT	0.403													C|||	2199	0.439097	0.7254	0.2997	5008	,	,		16911	0.5565		0.171	False		,,,				2504	0.3057				p.L519L		Atlas-SNP	.											MAP3K5,NS,carcinoma,0,1	MAP3K5	136	1	0			c.A1557G						PASS	.	C		2853,1553	487.8+/-361.0	929,995,279	115.0	109.0	111.0		1557	5.7	1.0	6	dbSNP_96	111	1499,7101	748.6+/-407.3	122,1255,2923	no	coding-synonymous	MAP3K5	NM_005923.3		1051,2250,3202	CC,CT,TT		17.4302,35.2474,33.4615		519/1375	136977568	4352,8654	2203	4300	6503	SO:0001819	synonymous_variant	4217	exon10			ATATATTAAAATT	U67156	CCDS5179.1	6q22.33	2011-06-09			ENSG00000197442	ENSG00000197442		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6857	protein-coding gene	gene with protein product	"""apoptosis signal regulating kinase 1"""	602448		MEKK5		9465908	Standard	NM_005923		Approved	MAPKKK5, ASK1	uc003qhc.3	Q99683	OTTHUMG00000015647	ENST00000359015.4:c.1557A>G	6.37:g.136977568T>C		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	63	5	0.0793651	NM_005923	A6NIA0|B4DGB2|Q5THN3|Q99461	Silent	SNP	ENST00000359015.4	37	CCDS5179.1																																																																																			T|0.613;C|0.387	0.387	strong		0.403	MAP3K5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042383.1		
NUTM2A	728118	hgsc.bcm.edu	37	10	88992641	88992641	+	Missense_Mutation	SNP	G	G	A	rs145500179	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr10:88992641G>A	ENST00000381707.2	+	5	2016	c.1633G>A	c.(1633-1635)Ggc>Agc	p.G545S	NUTM2A-AS1_ENST00000456104.1_RNA|NUTM2A_ENST00000381689.4_Missense_Mutation_p.G545S|NUTM2A-AS1_ENST00000451940.2_RNA	NM_001099338.1	NP_001092808.1	Q8IVF1	NTM2A_HUMAN	NUT family member 2A	545																	ACGGGAAGAGGGCGAAGTGAA	0.617													.|||	3976	0.79393	0.6974	0.8256	5008	,	,		17238	0.9563		0.7734	False		,,,				2504	0.7556				p.G545S		Atlas-SNP	.											FAM22D,colon,carcinoma,-2,2	FAM22A	20	2	0			c.G1633A						scavenged	.						7.0	9.0	8.0					10																	88992641		1545	3107	4652	SO:0001583	missense	728118	exon5			GAAGAGGGCGAAG		CCDS44452.1	10q23.2	2013-03-15	2013-03-14	2013-03-14	ENSG00000184923	ENSG00000184923			23438	protein-coding gene	gene with protein product			"""family with sequence similarity 22, member A"""	FAM22A			Standard	NM_001099338		Approved		uc001kek.3	Q8IVF1	OTTHUMG00000018670	ENST00000381707.2:c.1633G>A	10.37:g.88992641G>A	ENSP00000371126:p.Gly545Ser	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	97	8	0.0824742	NM_001099338	A6NMX5|C9JDI1|Q5VZW1	Missense_Mutation	SNP	ENST00000381707.2	37	CCDS44452.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	g|g	8.454|8.454	0.853843|0.853843	0.17106|0.17106	.|.	.|.	ENSG00000184923|ENSG00000184923	ENST00000451286|ENST00000381689;ENST00000381707;ENST00000416901;ENST00000432986	.|T;T	.|0.24723	.|1.84;2.64	1.18|1.18	1.18|1.18	0.20946|0.20946	.|Nuclear Testis protein, C-terminal (1);	1.216050|1.216050	0.05733|0.05733	N|N	0.599879|0.599879	T|T	0.26085|0.26085	0.0636|0.0636	L|L	0.51422|0.51422	1.61|1.61	0.80722|0.80722	P|P	0.0|0.0	.|P	.|0.43287	.|0.802	.|B	.|0.42959	.|0.403	T|T	0.31558|0.31558	-0.9939|-0.9939	5|9	.|0.37606	.|T	.|0.19	.|.	5.8963|5.8963	0.18941|0.18941	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|545	.|Q8IVF1	.|FA22A_HUMAN	E|S	322|545;545;472;22	.|ENSP00000371107:G545S;ENSP00000371126:G545S	.|ENSP00000371107:G545S	G|G	+|+	2|1	0|0	FAM22A|FAM22A	88982621|88982621	0.007000|0.007000	0.16637|0.16637	0.006000|0.006000	0.13384|0.13384	0.008000|0.008000	0.06430|0.06430	2.120000|2.120000	0.41968|0.41968	1.015000|1.015000	0.39444|0.39444	0.374000|0.374000	0.22700|0.22700	GGG|GGC	G|0.250;A|0.750	0.750	strong		0.617	NUTM2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049198.2	NM_001099338	
SEMA5A	9037	hgsc.bcm.edu	37	5	9052036	9052036	+	Missense_Mutation	SNP	C	C	T	rs139882587		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr5:9052036C>T	ENST00000382496.5	-	20	3459	c.2794G>A	c.(2794-2796)Ggg>Agg	p.G932R	MIR4636_ENST00000582271.1_RNA	NM_003966.2	NP_003957.2	Q13591	SEM5A_HUMAN	sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5A	932	TSP type-1 7. {ECO:0000255|PROSITE- ProRule:PRU00210}.				axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|blood vessel endothelial cell proliferation involved in sprouting angiogenesis (GO:0002043)|cell adhesion (GO:0007155)|cell chemotaxis (GO:0060326)|cell-cell signaling (GO:0007267)|diencephalon development (GO:0021536)|negative regulation of axon extension involved in axon guidance (GO:0048843)|negative regulation of cell adhesion (GO:0007162)|negative regulation of endothelial cell apoptotic process (GO:2000352)|nervous system development (GO:0007399)|patterning of blood vessels (GO:0001569)|positive chemotaxis (GO:0050918)|positive regulation of actin filament depolymerization (GO:0030836)|positive regulation of angiogenesis (GO:0045766)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of endothelial cell chemotaxis (GO:2001028)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of protein kinase B signaling (GO:0051897)|signal clustering (GO:1990256)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	axon guidance receptor activity (GO:0008046)|chondroitin sulfate proteoglycan binding (GO:0035373)|heparan sulfate proteoglycan binding (GO:0043395)|semaphorin receptor binding (GO:0030215)|syndecan binding (GO:0045545)			biliary_tract(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(13)|lung(40)|ovary(2)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	81						GTGGTGTTCCCGGAGCACTGG	0.552													C|||	1	0.000199681	0.0	0.0	5008	,	,		17425	0.0		0.0	False		,,,				2504	0.001				p.G932R		Atlas-SNP	.											SEMA5A,colon,carcinoma,+2,1	SEMA5A	236	1	0			c.G2794A						PASS	.	C	ARG/GLY	1,4405	2.1+/-5.4	0,1,2202	46.0	48.0	47.0		2794	4.2	0.6	5	dbSNP_134	47	2,8598	2.2+/-6.3	0,2,4298	yes	missense	SEMA5A	NM_003966.2	125	0,3,6500	TT,TC,CC		0.0233,0.0227,0.0231	probably-damaging	932/1075	9052036	3,13003	2203	4300	6503	SO:0001583	missense	9037	exon20			TGTTCCCGGAGCA	U52840	CCDS3875.1	5p15.2	2008-05-15			ENSG00000112902	ENSG00000112902		"""Semaphorins"""	10736	protein-coding gene	gene with protein product		609297		SEMAF		8817451, 9464278	Standard	NM_003966		Approved	semF	uc003jek.2	Q13591	OTTHUMG00000090501	ENST00000382496.5:c.2794G>A	5.37:g.9052036C>T	ENSP00000371936:p.Gly932Arg	Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	137	44	0.321168	NM_003966	D3DTC6|O60408|Q1RLL9	Missense_Mutation	SNP	ENST00000382496.5	37	CCDS3875.1	.	.	.	.	.	.	.	.	.	.	C	18.18	3.566959	0.65651	2.27E-4	2.33E-4	ENSG00000112902	ENST00000382496	T	0.22945	1.93	5.12	4.25	0.50352	.	0.000000	0.85682	D	0.000000	T	0.62233	0.2411	H	0.96301	3.8	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.73360	-0.4007	10	0.87932	D	0	.	11.7168	0.51659	0.0:0.9131:0.0:0.0869	.	932	Q13591	SEM5A_HUMAN	R	932	ENSP00000371936:G932R	ENSP00000371936:G932R	G	-	1	0	SEMA5A	9105036	1.000000	0.71417	0.601000	0.28877	0.266000	0.26442	7.573000	0.82421	1.287000	0.44583	0.655000	0.94253	GGG	C|1.000;T|0.000	0.000	strong		0.552	SEMA5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206989.2		
PRSS3	5646	hgsc.bcm.edu	37	9	33797828	33797828	+	Splice_Site	SNP	C	C	T	rs143209949		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr9:33797828C>T	ENST00000361005.5	+	3	373	c.373C>T	c.(373-375)Cgc>Tgc	p.R125C	PRSS3_ENST00000379405.3_Splice_Site_p.R68C|PRSS3_ENST00000429677.3_Splice_Site_p.R61C|RP11-133O22.6_ENST00000454429.2_RNA|PRSS3_ENST00000342836.4_Splice_Site_p.R82C	NM_007343.3	NP_031369	P35030	TRY3_HUMAN	protease, serine, 3	125	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				cobalamin metabolic process (GO:0009235)|digestion (GO:0007586)|endothelial cell migration (GO:0043542)|innate immune response (GO:0045087)|proteolysis (GO:0006508)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)|zymogen activation (GO:0031638)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			large_intestine(3)|lung(4)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(2)	13			LUSC - Lung squamous cell carcinoma(29;0.0176)			GCCCATCAGCCGCATCCAGGT	0.577													c|||	1	0.000199681	0.0	0.0	5008	,	,		21123	0.0		0.001	False		,,,				2504	0.0				p.R125C		Atlas-SNP	.											PRSS3_ENST00000361005,NS,carcinoma,-1,2	PRSS3	79	2	0			c.C373T						scavenged	.						106.0	97.0	100.0					9																	33797828		2203	4300	6503	SO:0001630	splice_region_variant	5646	exon3			ATCAGCCGCATCC		CCDS6545.1, CCDS47958.1, CCDS56570.1, CCDS56571.1	9p13	2010-05-07	2008-03-11		ENSG00000010438	ENSG00000010438	3.4.21.4	"""Serine peptidases / Serine peptidases"""	9486	protein-coding gene	gene with protein product	"""mesotrypsin"""	613578	"""protease, serine, 4 (trypsin 4, brain)"", ""protease, serine, 3 (mesotrypsin)"""	PRSS4		2326201, 8294000	Standard	NM_002771		Approved	TRY3, TRY4	uc003ztj.4	P35030	OTTHUMG00000019798	ENST00000361005.5:c.372-1C>T	9.37:g.33797828C>T		Somatic	82	2	0.0243902		WXS	Illumina HiSeq	Phase_I	73	5	0.0684932	NM_007343	A8CED1|A8CED3|A9Z1Y4|E7ES07|F8W7P3|P15951|Q15665|Q5VXV0|Q6ISJ4|Q9UQV3	Missense_Mutation	SNP	ENST00000361005.5	37	CCDS47958.1	.	.	.	.	.	.	.	.	.	.	C	12.80	2.045597	0.36085	.	.	ENSG00000010438	ENST00000361005;ENST00000457896;ENST00000342836;ENST00000429677;ENST00000379405	D;D;D;D;D	0.89196	-2.48;-2.48;-2.48;-2.48;-2.48	3.38	2.48	0.30137	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.193106	0.56097	D	0.000021	D	0.89729	0.6799	L	0.55213	1.73	0.51233	D	0.999918	D;D;D	0.76494	0.986;0.999;0.986	P;P;P	0.62885	0.765;0.908;0.701	D	0.87067	0.2157	10	0.66056	D	0.02	.	4.6046	0.12371	0.214:0.6633:0.0:0.1227	.	68;125;82	P35030-3;P35030;P35030-4	.;TRY3_HUMAN;.	C	125;80;82;61;68	ENSP00000354280:R125C;ENSP00000401249:R80C;ENSP00000340889:R82C;ENSP00000401828:R61C;ENSP00000368715:R68C	ENSP00000340889:R82C	R	+	1	0	PRSS3	33787828	0.896000	0.30565	0.865000	0.33974	0.073000	0.16967	1.513000	0.35823	0.551000	0.29008	-0.643000	0.03959	CGC	C|0.999;T|0.001	0.001	strong		0.577	PRSS3-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000052121.1	NM_002771	Missense_Mutation
TBC1D1	23216	hgsc.bcm.edu	37	4	38016395	38016395	+	Missense_Mutation	SNP	T	T	G	rs10501	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr4:38016395T>G	ENST00000261439.4	+	3	1038	c.683T>G	c.(682-684)gTg>gGg	p.V228G	TBC1D1_ENST00000508802.1_Missense_Mutation_p.V228G	NM_001253914.1|NM_001253915.1|NM_015173.3	NP_001240843.1|NP_001240844.1|NP_055988.2	Q86TI0	TBCD1_HUMAN	TBC1 (tre-2/USP6, BUB2, cdc16) domain family, member 1	228			V -> G (in dbSNP:rs10501).		membrane organization (GO:0061024)|regulation of protein localization (GO:0032880)	cytosol (GO:0005829)|nucleus (GO:0005634)	Rab GTPase activator activity (GO:0005097)			NS(1)|breast(3)|kidney(1)|large_intestine(5)|lung(19)|ovary(2)|prostate(2)|skin(2)|urinary_tract(1)	36						CAGGAGCCTGTGCGCAGGCCC	0.692													G|||	2897	0.578474	0.6422	0.487	5008	,	,		11341	0.7093		0.4284	False		,,,				2504	0.5767				p.V228G		Atlas-SNP	.											TBC1D1,NS,carcinoma,0,1	TBC1D1	94	1	0			c.T683G						PASS	.	G	GLY/VAL	2525,1759		779,967,396	12.0	15.0	14.0		683	0.3	0.0	4	dbSNP_52	14	3573,4971		790,1993,1489	no	missense	TBC1D1	NM_015173.2	109	1569,2960,1885	GG,GT,TT		41.8188,41.0598,47.5366	benign	228/1169	38016395	6098,6730	2142	4272	6414	SO:0001583	missense	23216	exon3			AGCCTGTGCGCAG	AB029031	CCDS33972.1, CCDS58897.1	4p14	2013-07-09			ENSG00000065882	ENSG00000065882			11578	protein-coding gene	gene with protein product		609850				10965142, 18258599	Standard	NM_015173		Approved	TBC, TBC1, KIAA1108	uc003gtb.3	Q86TI0	OTTHUMG00000150302	ENST00000261439.4:c.683T>G	4.37:g.38016395T>G	ENSP00000261439:p.Val228Gly	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	85	4	0.0470588	NM_015173	B7Z3D9|E9PGH8|Q96K82|Q9UPP4	Missense_Mutation	SNP	ENST00000261439.4	37	CCDS33972.1	1227	0.5618131868131868	307	0.6239837398373984	174	0.48066298342541436	426	0.7447552447552448	320	0.42216358839050133	G	0.134	-1.110455	0.01813	0.589402	0.418188	ENSG00000065882	ENST00000508802;ENST00000261439;ENST00000446803	T;T;T	0.17213	3.65;4.04;2.29	5.22	0.314	0.15847	Phosphotyrosine interaction domain (1);	0.609127	0.15462	N	0.261076	T	0.00012	0.0000	N	0.08118	0	0.51012	P	9.40000000000385E-5	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.12293	-1.0553	9	0.22109	T	0.4	-0.0107	4.0723	0.09887	0.0774:0.1785:0.3923:0.3518	rs10501;rs3188894;rs13113776;rs58439251	228;228;228	B9A6J6;E9PGH8;Q86TI0	.;.;TBCD1_HUMAN	G	228;228;99	ENSP00000423651:V228G;ENSP00000261439:V228G;ENSP00000396877:V99G	ENSP00000261439:V228G	V	+	2	0	TBC1D1	37692790	0.138000	0.22547	0.000000	0.03702	0.023000	0.10783	1.416000	0.34759	-0.122000	0.11766	-0.323000	0.08544	GTG	T|0.448;G|0.552	0.552	strong		0.692	TBC1D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317443.2	NM_015173	
KLRC3	3823	hgsc.bcm.edu	37	12	10588444	10588444	+	Missense_Mutation	SNP	G	G	C	rs111237999	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr12:10588444G>C	ENST00000539033.1	-	1	156	c.142C>G	c.(142-144)Cct>Gct	p.P48A	KLRC2_ENST00000536833.2_Intron|KLRC2_ENST00000381902.2_Missense_Mutation_p.P48A|KLRC2_ENST00000381901.1_Missense_Mutation_p.P48A																							TTCAGGGAAGGATTTTGAAGA	0.363													G|||	125	0.0249601	0.0386	0.0101	5008	,	,		16153	0.0298		0.0268	False		,,,				2504	0.0102				p.P48A		Atlas-SNP	.											KLRC2,NS,carcinoma,+1,1	KLRC2	29	1	0			c.C142G						scavenged	.						94.0	104.0	101.0					12																	10588444		1994	3988	5982	SO:0001583	missense	3822	exon1			GGGAAGGATTTTG																												ENST00000539033.1:c.142C>G	12.37:g.10588444G>C	ENSP00000437563:p.Pro48Ala	Somatic	242	13	0.053719		WXS	Illumina HiSeq	Phase_I	213	17	0.0798122	NM_002260		Missense_Mutation	SNP	ENST00000539033.1	37		.	.	.	.	.	.	.	.	.	.	G	0	-2.662523	0.00107	.	.	ENSG00000255641;ENSG00000205809;ENSG00000205809	ENST00000539033;ENST00000381902;ENST00000381901	T;T;T	0.04119	3.7;3.7;3.7	2.57	-1.4	0.08968	.	0.714893	0.12708	N	0.445758	T	0.01222	0.0040	N	0.00637	-1.305	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	0.46925	-0.9156	10	0.02654	T	1	.	9.8776	0.41213	0.0:0.3246:0.6754:0.0	rs34194304	34;48;48	Q3KQS7;P26717;F5H6K3	.;NKG2C_HUMAN;.	A	48	ENSP00000437563:P48A;ENSP00000371327:P48A;ENSP00000371326:P48A	ENSP00000371326:P48A	P	-	1	0	KLRC2;RP11-277P12.6	10479711	0.000000	0.05858	0.020000	0.16555	0.010000	0.07245	-0.911000	0.04050	-0.034000	0.13713	-1.406000	0.01132	CCT	.	.	weak		0.363	NKG2-E-001	KNOWN	basic|appris_principal|readthrough_transcript	protein_coding	protein_coding	OTTHUMT00000400274.1		
MAN1B1	11253	hgsc.bcm.edu	37	9	139981546	139981546	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr9:139981546C>T	ENST00000371589.4	+	1	168	c.95C>T	c.(94-96)gCc>gTc	p.A32V	MAN1B1_ENST00000474902.1_5'Flank|AL807752.1_ENST00000596585.1_5'Flank	NM_016219.4	NP_057303.2	Q9UKM7	MA1B1_HUMAN	mannosidase, alpha, class 1B, member 1	32					cellular protein metabolic process (GO:0044267)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|oligosaccharide metabolic process (GO:0009311)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum quality control compartment (GO:0044322)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|vesicle (GO:0031982)	calcium ion binding (GO:0005509)|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity (GO:0004571)			autonomic_ganglia(1)|central_nervous_system(2)|kidney(1)|large_intestine(2)|liver(2)|lung(4)|ovary(2)	14	all_cancers(76;0.0926)	Myeloproliferative disorder(178;0.0511)	STAD - Stomach adenocarcinoma(284;0.0878)	OV - Ovarian serous cystadenocarcinoma(145;3.08e-05)|Epithelial(140;0.000513)		TGGGCCGTCGCCACCACTGTA	0.652																																					p.A32V		Atlas-SNP	.											.	MAN1B1	40	.	0			c.C95T						PASS	.						10.0	13.0	12.0					9																	139981546		2178	4265	6443	SO:0001583	missense	11253	exon1			CCGTCGCCACCAC	AF145732	CCDS7029.1	9q34.3	2014-05-27			ENSG00000177239	ENSG00000177239			6823	protein-coding gene	gene with protein product	"""endoplasmic reticulum alpha-mannosidase 1"", ""alpha 1,2-mannosidase"", ""endoplasmic reticulum mannosyl-oligosaccharide 1,2-alpha-mannosidase 1"", ""ER alpha 1,2-mannosidase"", ""Man9GlcNAc2-specific processing alpha-mannosidase"""	604346				10409699, 10521544	Standard	NM_016219		Approved	MANA-ER, MRT15	uc004cld.3	Q9UKM7	OTTHUMG00000020978	ENST00000371589.4:c.95C>T	9.37:g.139981546C>T	ENSP00000360645:p.Ala32Val	Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	48	12	0.25	NM_016219	Q5VSG3|Q9BRS9|Q9Y5K7	Missense_Mutation	SNP	ENST00000371589.4	37	CCDS7029.1	.	.	.	.	.	.	.	.	.	.	C	10.55	1.382251	0.24944	.	.	ENSG00000177239	ENST00000371589	T	0.74106	-0.81	3.33	-0.544	0.11847	.	.	.	.	.	T	0.48660	0.1512	N	0.08118	0	0.09310	N	0.999995	B	0.02656	0.0	B	0.04013	0.001	T	0.36237	-0.9756	9	0.72032	D	0.01	.	2.3432	0.04265	0.404:0.2871:0.0:0.3089	.	32	Q9UKM7	MA1B1_HUMAN	V	32	ENSP00000360645:A32V	ENSP00000360645:A32V	A	+	2	0	MAN1B1	139101367	0.002000	0.14202	0.000000	0.03702	0.031000	0.12232	0.358000	0.20216	-0.242000	0.09667	0.462000	0.41574	GCC	.	.	none		0.652	MAN1B1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055294.2	NM_016219	
MUC4	4585	hgsc.bcm.edu	37	3	195509170	195509170	+	Missense_Mutation	SNP	A	A	G	rs71634716|rs202189117	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr3:195509170A>G	ENST00000463781.3	-	2	9740	c.9281T>C	c.(9280-9282)cTt>cCt	p.L3094P	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.L3094P	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)		TACTGAGGAAAGGCTGGTGAC	0.602																																					p.L3094P		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,-1,1	MUC4	1505	1	0			c.T9281C						scavenged	.						13.0	10.0	11.0					3																	195509170		667	1550	2217	SO:0001583	missense	4585	exon2			GAGGAAAGGCTGG	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.9281T>C	3.37:g.195509170A>G	ENSP00000417498:p.Leu3094Pro	Somatic	45	4	0.0888889		WXS	Illumina HiSeq	Phase_I	53	5	0.0943396	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	6.319	0.427039	0.11987	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.37235	1.27;1.21	1.18	1.18	0.20946	.	.	.	.	.	T	0.14485	0.0350	N	0.14661	0.345	0.30615	N	0.75912	P	0.47604	0.898	B	0.34180	0.177	T	0.13737	-1.0498	8	.	.	.	.	4.1756	0.10349	0.6345:0.3655:0.0:0.0	.	2966	E7ESK3	.	P	3094	ENSP00000417498:L3094P;ENSP00000420243:L3094P	.	L	-	2	0	MUC4	196993949	.	.	0.016000	0.15963	0.000000	0.00434	.	.	0.577000	0.29470	0.000000	0.15137	CTT	A|0.994;G|0.006	0.006	strong		0.602	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
ADAMTS20	80070	hgsc.bcm.edu	37	12	43769276	43769276	+	Silent	SNP	T	T	C	rs10880473	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr12:43769276T>C	ENST00000389420.3	-	36	5351	c.5352A>G	c.(5350-5352)agA>agG	p.R1784R		NM_025003.3	NP_079279.3	P59510	ATS20_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 20	1784	GON. {ECO:0000255|PROSITE- ProRule:PRU00383}.				extracellular matrix organization (GO:0030198)|negative regulation of apoptotic process (GO:0043066)|positive regulation of melanocyte differentiation (GO:0045636)|positive regulation of signal transduction (GO:0009967)	extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(6)|endometrium(3)|kidney(4)|large_intestine(11)|liver(1)|lung(43)|ovary(4)|pancreas(3)|prostate(5)|skin(12)|upper_aerodigestive_tract(1)|urinary_tract(1)	95	all_cancers(12;2.6e-05)|Lung SC(27;0.184)	Lung NSC(34;0.0569)|all_lung(34;0.129)		GBM - Glioblastoma multiforme(48;0.0473)		AGTCTTCCCTTCTACTCCCAT	0.348													C|||	1121	0.223842	0.4266	0.1239	5008	,	,		18065	0.1002		0.1998	False		,,,				2504	0.1728				p.R1784R		Atlas-SNP	.											ADAMTS20_ENST00000389420,neck,malignant_melanoma,-2,1	ADAMTS20	635	1	0			c.A5352G						PASS	.	C		1647,2759	659.9+/-400.6	316,1015,872	156.0	153.0	154.0		5352	2.0	1.0	12	dbSNP_120	154	1768,6832	734.1+/-406.9	182,1404,2714	no	coding-synonymous	ADAMTS20	NM_025003.3		498,2419,3586	CC,CT,TT		20.5581,37.3808,26.2571		1784/1911	43769276	3415,9591	2203	4300	6503	SO:0001819	synonymous_variant	80070	exon36			TTCCCTTCTACTC	AF488804	CCDS31778.2	12q12	2005-08-19	2005-08-19			ENSG00000173157		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	17178	protein-coding gene	gene with protein product		611681	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 20"""			12514189, 12562771	Standard	NM_025003		Approved	GON-1	uc010skx.2	P59510		ENST00000389420.3:c.5352A>G	12.37:g.43769276T>C		Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	104	5	0.0480769	NM_025003	A6NNC9|J3QT00	Silent	SNP	ENST00000389420.3	37	CCDS31778.2																																																																																			T|0.747;C|0.253	0.253	strong		0.348	ADAMTS20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403643.1	NM_025003	
ARHGAP12	94134	hgsc.bcm.edu	37	10	32128611	32128611	+	Missense_Mutation	SNP	A	A	G	rs2808096	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr10:32128611A>G	ENST00000344936.2	-	8	1559	c.1325T>C	c.(1324-1326)tTt>tCt	p.F442S	ARHGAP12_ENST00000311380.4_Missense_Mutation_p.F395S|ARHGAP12_ENST00000375245.4_Missense_Mutation_p.F395S|ARHGAP12_ENST00000396144.4_Missense_Mutation_p.F442S|ARHGAP12_ENST00000375250.5_Intron	NM_001270697.1|NM_018287.6	NP_001257626.1|NP_060757.4	Q8IWW6	RHG12_HUMAN	Rho GTPase activating protein 12	442			F -> S (in dbSNP:rs2808096).		morphogenesis of an epithelial sheet (GO:0002011)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)			NS(1)|breast(3)|endometrium(2)|kidney(1)|large_intestine(11)|lung(10)|skin(1)|urinary_tract(2)	31		Prostate(175;0.0199)				ATTTTCAGGAAAGCAGGGTTT	0.343													A|||	1161	0.231829	0.0545	0.2954	5008	,	,		13632	0.4127		0.2048	False		,,,				2504	0.2679				p.F442S		Atlas-SNP	.											.	ARHGAP12	79	.	0			c.T1325C						PASS	.	A	SER/PHE	371,4035	186.4+/-213.3	16,339,1848	109.0	110.0	110.0		1325	3.2	1.0	10	dbSNP_100	110	1824,6776	326.4+/-317.4	190,1444,2666	yes	missense	ARHGAP12	NM_018287.5	155	206,1783,4514	GG,GA,AA		21.2093,8.4203,16.8768	benign	442/847	32128611	2195,10811	2203	4300	6503	SO:0001583	missense	94134	exon8			TCAGGAAAGCAGG	AY033594	CCDS7170.1, CCDS59214.1, CCDS59215.1, CCDS59216.1, CCDS73082.1	10p11.22	2013-01-10			ENSG00000165322	ENSG00000165322		"""Rho GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"""	16348	protein-coding gene	gene with protein product		610577				11854031	Standard	NM_001270695		Approved	FLJ20737, FLJ10971, FLJ21785	uc001ivz.2	Q8IWW6	OTTHUMG00000017911	ENST00000344936.2:c.1325T>C	10.37:g.32128611A>G	ENSP00000345808:p.Phe442Ser	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	68	4	0.0588235	NM_001270695	B1ANY0|B1ANY1|B1ANY2|Q504X1|Q86UB3|Q8IWW7|Q8N3L1|Q9NT76	Missense_Mutation	SNP	ENST00000344936.2	37	CCDS7170.1	505	0.23122710622710624	28	0.056910569105691054	89	0.24585635359116023	219	0.38286713286713286	169	0.22295514511873352	A	11.71	1.718440	0.30503	0.084203	0.212093	ENSG00000165322	ENST00000311380;ENST00000344936;ENST00000396144;ENST00000375245	T;T;T;T	0.35048	1.33;1.33;1.33;1.33	5.51	3.15	0.36227	.	0.228703	0.38548	N	0.001653	T	0.00012	0.0000	N	0.08118	0	0.36264	P	0.145235	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.001;0.001	T	0.48091	-0.9065	9	0.20046	T	0.44	.	6.4215	0.21746	0.7804:0.0:0.0739:0.1457	rs2808096;rs17582209;rs52793660;rs2808096	442;442;395	Q504X1;Q8IWW6;Q8IWW6-3	.;RHG12_HUMAN;.	S	395;442;442;395	ENSP00000310984:F395S;ENSP00000345808:F442S;ENSP00000379448:F442S;ENSP00000364394:F395S	ENSP00000310984:F395S	F	-	2	0	ARHGAP12	32168617	1.000000	0.71417	0.999000	0.59377	0.997000	0.91878	1.817000	0.39002	0.443000	0.26582	0.533000	0.62120	TTT	G|0.199;N|0.000	0.199	strong		0.343	ARHGAP12-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000047465.1		
EIF2AK4	440275	hgsc.bcm.edu	37	15	40259848	40259848	+	Missense_Mutation	SNP	A	A	C	rs2291627	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr15:40259848A>C	ENST00000263791.5	+	9	1364	c.1321A>C	c.(1321-1323)Att>Ctt	p.I441L	EIF2AK4_ENST00000382727.2_Missense_Mutation_p.I441L|EIF2AK4_ENST00000559624.1_Missense_Mutation_p.I441L	NM_001013703.2	NP_001013725.2	Q9P2K8	E2AK4_HUMAN	eukaryotic translation initiation factor 2 alpha kinase 4	441	Protein kinase 1. {ECO:0000255|PROSITE- ProRule:PRU00159}.		I -> L (in dbSNP:rs2291627). {ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:17974005}.		cellular response to starvation (GO:0009267)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of translation (GO:0017148)|protein phosphorylation (GO:0006468)|regulation of translational initiation (GO:0006446)|regulation of translational initiation in response to stress (GO:0043558)	cytosolic ribosome (GO:0022626)	ATP binding (GO:0005524)|eukaryotic translation initiation factor 2alpha kinase activity (GO:0004694)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(2)|endometrium(1)|kidney(3)|large_intestine(8)|lung(18)|ovary(1)|prostate(3)|skin(2)|stomach(1)	40		all_cancers(109;1.05e-19)|all_epithelial(112;4.38e-17)|Lung NSC(122;1.09e-12)|all_lung(180;3.56e-11)|Melanoma(134;0.0575)|Ovarian(310;0.0826)|Colorectal(260;0.119)		GBM - Glioblastoma multiforme(113;5.31e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0616)		CACCGTCAAGATTACGGACTA	0.468													A|||	1239	0.247404	0.233	0.134	5008	,	,		23651	0.5387		0.0924	False		,,,				2504	0.2065				p.I441L		Atlas-SNP	.											.	EIF2AK4	107	.	0			c.A1321C						PASS	.	A	LEU/ILE	762,3232		68,626,1303	107.0	105.0	106.0		1321	4.5	1.0	15	dbSNP_100	106	739,7611		33,673,3469	yes	missense	EIF2AK4	NM_001013703.2	5	101,1299,4772	CC,CA,AA		8.8503,19.0786,12.1598	benign	441/1650	40259848	1501,10843	1997	4175	6172	SO:0001583	missense	440275	exon9			GTCAAGATTACGG	AB037759	CCDS42016.1	15q13.3	2008-08-18				ENSG00000128829			19687	protein-coding gene	gene with protein product		609280				10504407	Standard	XM_005254392		Approved	GCN2, KIAA1338	uc001zkm.1	Q9P2K8		ENST00000263791.5:c.1321A>C	15.37:g.40259848A>C	ENSP00000263791:p.Ile441Leu	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	124	8	0.0645161	NM_001013703	C9JEC4|Q69YL7|Q6DC97|Q96GN6|Q9H5K1|Q9NSQ3|Q9NSZ5|Q9UJ56	Missense_Mutation	SNP	ENST00000263791.5	37	CCDS42016.1	531	0.24313186813186813	115	0.23373983739837398	45	0.12430939226519337	298	0.5209790209790209	73	0.09630606860158311	A	4.744	0.138332	0.09083	0.190786	0.088503	ENSG00000128829	ENST00000263791;ENST00000382727	T;T	0.68903	-0.36;-0.36	5.58	4.46	0.54185	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.323593	0.34025	N	0.004327	T	0.00012	0.0000	N	0.02225	-0.63	0.35081	P	0.236591	B;B	0.09022	0.001;0.002	B;B	0.12156	0.007;0.002	T	0.43621	-0.9380	9	0.02654	T	1	-16.4002	4.9105	0.13820	0.5452:0.2912:0.1637:0.0	rs2291627;rs52819941;rs61355221;rs2291627	441;441	Q9P2K8;Q9P2K8-3	E2AK4_HUMAN;.	L	441	ENSP00000263791:I441L;ENSP00000372174:I441L	ENSP00000263791:I441L	I	+	1	0	EIF2AK4	38047140	1.000000	0.71417	0.972000	0.41901	0.798000	0.45092	1.331000	0.33793	1.052000	0.40392	0.533000	0.62120	ATT	C|0.219;N|0.000	0.219	strong		0.468	EIF2AK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418395.1		
KIF20B	9585	hgsc.bcm.edu	37	10	91503660	91503660	+	Silent	SNP	A	A	G	rs1126480	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr10:91503660A>G	ENST00000371728.3	+	22	4076	c.4011A>G	c.(4009-4011)aaA>aaG	p.K1337K	KIF20B_ENST00000416354.1_Silent_p.K1367K|KIF20B_ENST00000394289.2_Silent_p.K1337K|KIF20B_ENST00000478929.1_3'UTR|KIF20B_ENST00000260753.4_Silent_p.K1297K	NM_001284259.1	NP_001271188.1	Q96Q89	KI20B_HUMAN	kinesin family member 20B	1337					ATP catabolic process (GO:0006200)|cell cycle arrest (GO:0007050)|microtubule-based movement (GO:0007018)|mitotic nuclear division (GO:0007067)|neural tube closure (GO:0001843)|regulation of establishment of cell polarity (GO:2000114)|regulation of establishment of protein localization (GO:0070201)|regulation of mitosis (GO:0007088)|regulation of neuron migration (GO:2001222)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|WW domain binding (GO:0050699)			endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(20)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)	58						TAGATATGAAACAGCGAACCA	0.308													A|||	1772	0.353834	0.4697	0.2147	5008	,	,		14368	0.3085		0.2326	False		,,,				2504	0.4673				p.K1297K		Atlas-SNP	.											KIF20B_ENST00000416354,adrenal_gland,adrenal_cortical_adenoma,0,2	KIF20B	191	2	0			c.A3891G						scavenged	.	A		2024,2380	550.2+/-378.0	472,1080,650	81.0	92.0	88.0		3891	5.4	1.0	10	dbSNP_86	88	2002,6596	347.3+/-326.5	221,1560,2518	no	coding-synonymous	KIF20B	NM_016195.2		693,2640,3168	GG,GA,AA		23.2845,45.9582,30.9645		1297/1781	91503660	4026,8976	2202	4299	6501	SO:0001819	synonymous_variant	9585	exon22			TATGAAACAGCGA	L16782	CCDS7407.1, CCDS60590.1	10q23.31	2009-08-06	2008-07-31	2008-07-31	ENSG00000138182	ENSG00000138182			7212	protein-coding gene	gene with protein product	"""cancer/testis antigen 90"""	605498	"""M-phase phosphoprotein 1"""	MPHOSPH1		8885239, 8290587, 11470801	Standard	NM_016195		Approved	MPP1, KRMP1, CT90	uc001kgr.1	Q96Q89	OTTHUMG00000018725	ENST00000371728.3:c.4011A>G	10.37:g.91503660A>G		Somatic	501	0	0		WXS	Illumina HiSeq	Phase_I	498	10	0.0200803	NM_016195	A8MXM7|O43277|Q09471|Q2KQ73|Q32NE1|Q561V3|Q58EX8|Q5T9M8|Q5T9M9|Q5T9N0|Q5T9N1|Q7KZ68|Q7Z5E0|Q7Z5E1|Q7Z6M9|Q86X82|Q9H3R8|Q9H6Q9|Q9H755|Q9NTC1|Q9UFR5	Silent	SNP	ENST00000371728.3	37																																																																																				A|0.701;G|0.299	0.299	strong		0.308	KIF20B-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000049330.1	NM_016195	
HS3ST2	9956	hgsc.bcm.edu	37	16	22826243	22826243	+	Silent	SNP	C	C	T			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr16:22826243C>T	ENST00000261374.3	+	1	746	c.312C>T	c.(310-312)tcC>tcT	p.S104S		NM_006043.1	NP_006034.1	Q9Y278	HS3S2_HUMAN	heparan sulfate (glucosamine) 3-O-sulfotransferase 2	104					carbohydrate metabolic process (GO:0005975)|circadian rhythm (GO:0007623)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	[heparan sulfate]-glucosamine 3-sulfotransferase 2 activity (GO:0033871)|sulfotransferase activity (GO:0008146)			breast(2)|kidney(1)|large_intestine(5)|liver(2)|lung(5)|ovary(1)|pancreas(2)|skin(1)	19				GBM - Glioblastoma multiforme(48;0.0299)		CCAACCACTCCGGCTCACCCA	0.716																																					p.S104S		Atlas-SNP	.											.	HS3ST2	59	.	0			c.C312T						PASS	.						7.0	9.0	8.0					16																	22826243		2158	4266	6424	SO:0001819	synonymous_variant	9956	exon1			CCACTCCGGCTCA	AF105374	CCDS10606.1	16p12	2008-02-05			ENSG00000122254	ENSG00000122254	2.8.2.23	"""Sulfotransferases, membrane-bound"""	5195	protein-coding gene	gene with protein product		604056				9988767	Standard	NM_006043		Approved	3OST2	uc002dli.3	Q9Y278	OTTHUMG00000094785	ENST00000261374.3:c.312C>T	16.37:g.22826243C>T		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	66	21	0.318182	NM_006043	Q52LZ1	Silent	SNP	ENST00000261374.3	37	CCDS10606.1																																																																																			.	.	none		0.716	HS3ST2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211598.1	NM_006043	
KRTAP4-11	653240	hgsc.bcm.edu	37	17	39274172	39274172	+	Silent	SNP	G	G	T			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr17:39274172G>T	ENST00000391413.2	-	1	434	c.396C>A	c.(394-396)ccC>ccA	p.P132P		NM_033059.3	NP_149048.2	Q9BYQ6	KR411_HUMAN	keratin associated protein 4-11	132	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)			ggcagcaggtgggctggcagc	0.672																																					p.P132P		Atlas-SNP	.											KRTAP4-11,NS,carcinoma,-2,2	KRTAP4-11	94	2	0			c.C396A						scavenged	.						7.0	12.0	11.0					17																	39274172		675	1578	2253	SO:0001819	synonymous_variant	653240	exon1			GCAGGTGGGCTGG	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.396C>A	17.37:g.39274172G>T		Somatic	68	1	0.0147059		WXS	Illumina HiSeq	Phase_I	64	3	0.046875	NM_033059	A0AUY2	Silent	SNP	ENST00000391413.2	37	CCDS45675.1																																																																																			.	.	none		0.672	KRTAP4-11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257690.1		
NPEPPS	9520	hgsc.bcm.edu	37	17	45669359	45669359	+	Missense_Mutation	SNP	T	T	G	rs200616431		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr17:45669359T>G	ENST00000322157.4	+	11	1535	c.1298T>G	c.(1297-1299)tTt>tGt	p.F433C	NPEPPS_ENST00000525037.1_3'UTR|NPEPPS_ENST00000530173.1_Missense_Mutation_p.F429C|NPEPPS_ENST00000544660.1_Missense_Mutation_p.F353C	NM_006310.3	NP_006301.3	P55786	PSA_HUMAN	aminopeptidase puromycin sensitive	433					antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular response to hypoxia (GO:0071456)|protein polyubiquitination (GO:0000209)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.F433C(1)		breast(1)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(6)|lung(7)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	27						GATGAGATATTTGATGCTATA	0.383																																					p.F433C		Atlas-SNP	.											NPEPPS,mouth,carcinoma,0,1	NPEPPS	59	1	1	Substitution - Missense(1)	upper_aerodigestive_tract(1)	c.T1298G						scavenged	.						123.0	78.0	93.0					17																	45669359		2020	4149	6169	SO:0001583	missense	9520	exon11			AGATATTTGATGC	Y07701	CCDS45721.1	17q12-q21	2008-07-18			ENSG00000141279	ENSG00000141279	3.4.11.2		7900	protein-coding gene	gene with protein product	"""puromycin-sensitive aminopeptidase"", ""metalloproteinase MP100"""	606793				9048733, 10329370	Standard	NM_006310		Approved	PSA, MP100	uc002ilr.4	P55786	OTTHUMG00000165471	ENST00000322157.4:c.1298T>G	17.37:g.45669359T>G	ENSP00000320324:p.Phe433Cys	Somatic	428	0	0		WXS	Illumina HiSeq	Phase_I	387	4	0.0103359	NM_006310	B7Z463|Q6P145|Q9NP16|Q9UEM2	Missense_Mutation	SNP	ENST00000322157.4	37	CCDS45721.1	.	.	.	.	.	.	.	.	.	.	T	24.3	4.519381	0.85495	.	.	ENSG00000141279	ENST00000530173;ENST00000322157;ENST00000539572;ENST00000544660;ENST00000527964;ENST00000527360	T;T;T;T;T	0.09911	2.93;2.93;2.93;2.93;2.93	5.51	5.51	0.81932	Peptidase M1, membrane alanine aminopeptidase, N-terminal (2);	0.000000	0.85682	D	0.000000	T	0.54532	0.1864	H	0.99435	4.565	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	T	0.76427	-0.2963	10	0.87932	D	0	.	15.6257	0.76855	0.0:0.0:0.0:1.0	.	433;429;433	A6NEC2;E9PLK3;P55786	PSAL_HUMAN;.;PSA_HUMAN	C	429;433;420;353;116;130	ENSP00000433287:F429C;ENSP00000320324:F433C;ENSP00000442461:F353C;ENSP00000435639:F116C;ENSP00000435966:F130C	ENSP00000320324:F433C	F	+	2	0	NPEPPS	43024358	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.850000	0.86915	2.099000	0.63709	0.528000	0.53228	TTT	T|1.000;|0.000	.	weak		0.383	NPEPPS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384269.1	NM_006310	
DNAH14	127602	hgsc.bcm.edu	37	1	225528183	225528183	+	Missense_Mutation	SNP	C	C	A	rs377250670|rs3856145	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr1:225528183C>A	ENST00000445597.2	+	47	7770	c.7770C>A	c.(7768-7770)gaC>gaA	p.D2590E	DNAH14_ENST00000439375.2_Missense_Mutation_p.D3393E|DNAH14_ENST00000430092.1_Missense_Mutation_p.D3393E			Q0VDD8	DYH14_HUMAN	dynein, axonemal, heavy chain 14	2590					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						CAGAAATAGACAACCCCCATT	0.318													C|||	2653	0.529752	0.643	0.4697	5008	,	,		17622	0.5089		0.4046	False		,,,				2504	0.5695				p.D3393E		Atlas-SNP	.											.	DNAH14	300	.	0			c.C10179A						PASS	.	C	GLU/ASP	846,538		270,306,116	113.0	99.0	103.0		10179	0.7	1.0	1	dbSNP_108	103	1403,1779		323,757,511	yes	missense	DNAH14	NM_001373.1	45	593,1063,627	AA,AC,CC		44.0918,38.8728,49.2554	possibly-damaging	3393/4516	225528183	2249,2317	692	1591	2283	SO:0001583	missense	127602	exon67			AATAGACAACCCC	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.7770C>A	1.37:g.225528183C>A	ENSP00000409472:p.Asp2590Glu	Somatic	351	0	0		WXS	Illumina HiSeq	Phase_I	253	12	0.0474308	NM_001373	A6NG62|A6NNL2|Q0VDD9|Q4VXC7|Q4VXG4|Q4VXG5|Q5VU33|Q5VU34	Missense_Mutation	SNP	ENST00000445597.2	37		1057	0.483974358974359	305	0.6199186991869918	165	0.4558011049723757	281	0.49125874125874125	306	0.40369393139841686	C	13.41	2.229518	0.39399	0.611272	0.440918	ENSG00000185842	ENST00000445597;ENST00000430092;ENST00000439375	T;T;T	0.21191	2.02;2.02;2.02	5.22	0.724	0.18236	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.99999999854566	B	0.31817	0.341	B	0.32762	0.152	T	0.33214	-0.9877	7	0.32370	T	0.25	.	1.4675	0.02408	0.2894:0.3987:0.141:0.1709	rs3856145;rs52794541;rs58846503;rs3856145	3393	Q0VDD8-4	.	E	2590;3393;3393	ENSP00000409472:D2590E;ENSP00000414402:D3393E;ENSP00000392061:D3393E	ENSP00000414402:D3393E	D	+	3	2	DNAH14	223594806	1.000000	0.71417	0.981000	0.43875	0.977000	0.68977	0.462000	0.21956	-0.062000	0.13088	0.508000	0.49915	GAC	C|0.498;A|0.500	0.500	strong		0.318	DNAH14-007	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000331217.3	XM_059166	
MYOM1	8736	hgsc.bcm.edu	37	18	3215156	3215156	+	Silent	SNP	C	C	G	rs386800438|rs1662316	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr18:3215156C>G	ENST00000356443.4	-	2	399	c.66G>C	c.(64-66)gtG>gtC	p.V22V	MYOM1_ENST00000400569.3_Silent_p.V22V|MYOM1_ENST00000261606.7_Silent_p.V22V|RP13-270P17.2_ENST00000580139.1_RNA	NM_003803.3|NM_019856.1	NP_003794.3|NP_062830.1	P52179	MYOM1_HUMAN	myomesin 1	22			V -> L (in dbSNP:rs1791085).		muscle contraction (GO:0006936)	M band (GO:0031430)|striated muscle myosin thick filament (GO:0005863)	identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|structural constituent of muscle (GO:0008307)			NS(2)|autonomic_ganglia(1)|central_nervous_system(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(20)|ovary(4)|pancreas(1)|prostate(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	77						CGGTGCTGCGCACGTCCTTGT	0.622													G|||	646	0.128994	0.1346	0.0879	5008	,	,		16440	0.1865		0.0934	False		,,,				2504	0.1278				p.V22V		Atlas-SNP	.											.	MYOM1	192	.	0			c.G66C						PASS	.	G	,	504,3708		30,444,1632	56.0	60.0	59.0		66,66	-11.3	0.0	18	dbSNP_89	59	728,7756		30,668,3544	no	coding-synonymous,coding-synonymous	MYOM1	NM_003803.3,NM_019856.1	,	60,1112,5176	GG,GC,CC		8.5809,11.9658,9.7038	,	22/1686,22/1590	3215156	1232,11464	2106	4242	6348	SO:0001819	synonymous_variant	8736	exon2			GCTGCGCACGTCC	AF185573	CCDS45823.1, CCDS45824.1	18p11.31	2014-09-17	2012-10-17		ENSG00000101605	ENSG00000101605		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	7613	protein-coding gene	gene with protein product	"""skelemin"""	603508	"""myomesin 1 (skelemin) (185kD)"", ""myomesin 1 (skelemin) 185kDa"", ""myomesin 1, 185kDa"""			9806852	Standard	NM_019856		Approved		uc002klp.3	P52179	OTTHUMG00000178209	ENST00000356443.4:c.66G>C	18.37:g.3215156C>G		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	100	7	0.07	NM_003803	Q14BD6|Q6H969|Q6ZUU0	Silent	SNP	ENST00000356443.4	37	CCDS45824.1																																																																																			C|0.891;G|0.109	0.109	strong		0.622	MYOM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441037.2	NM_003803	
NEB	4703	hgsc.bcm.edu	37	2	152527608	152527608	+	Missense_Mutation	SNP	C	C	T	rs34577613	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr2:152527608C>T	ENST00000172853.10	-	38	4582	c.4435G>A	c.(4435-4437)Gtc>Atc	p.V1479I	NEB_ENST00000604864.1_Missense_Mutation_p.V1479I|NEB_ENST00000427231.2_Missense_Mutation_p.V1479I|NEB_ENST00000603639.1_Missense_Mutation_p.V1479I|NEB_ENST00000409198.1_Missense_Mutation_p.V1479I|NEB_ENST00000397345.3_Missense_Mutation_p.V1479I			P20929	NEBU_HUMAN	nebulin	1479			V -> I (in dbSNP:rs34577613).		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)	p.V1479I(1)		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)		GTGAACTTGACGGTATCTGGG	0.483													T|||	1679	0.335264	0.4546	0.1095	5008	,	,		21763	0.5754		0.1223	False		,,,				2504	0.3057				p.V1479I		Atlas-SNP	.											NEB,NS,carcinoma,0,1	NEB	1697	1	1	Substitution - Missense(1)	stomach(1)	c.G4435A						PASS	.	T	ILE/VAL,ILE/VAL,ILE/VAL	1503,2705		261,981,862	164.0	163.0	163.0		4435,4435,4435	4.2	1.0	2	dbSNP_126	163	920,7532		58,804,3364	yes	missense,missense,missense	NEB	NM_001164507.1,NM_001164508.1,NM_004543.4	29,29,29	319,1785,4226	TT,TC,CC		10.885,35.7177,19.139	benign,benign,benign	1479/8526,1479/8526,1479/6670	152527608	2423,10237	2104	4226	6330	SO:0001583	missense	4703	exon38			ACTTGACGGTATC	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.4435G>A	2.37:g.152527608C>T	ENSP00000172853:p.Val1479Ile	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	149	8	0.0536913	NM_004543	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Missense_Mutation	SNP	ENST00000172853.10	37		700	0.32051282051282054	243	0.49390243902439024	46	0.1270718232044199	322	0.5629370629370629	89	0.11741424802110818	T	5.418	0.262254	0.10239	0.357177	0.10885	ENSG00000183091	ENST00000409198;ENST00000397345;ENST00000427231;ENST00000172853	T;T;T;T	0.05081	3.5;3.53;3.53;3.54	5.42	4.25	0.50352	.	0.288297	0.32671	N	0.005787	T	0.00012	0.0000	N	0.00707	-1.245	0.09310	P	0.9999999999754821	B	0.02656	0.0	B	0.04013	0.001	T	0.26883	-1.0090	9	0.10902	T	0.67	.	7.0714	0.25181	0.0:0.138:0.1258:0.7362	rs34577613;rs60727639	1479	P20929	NEBU_HUMAN	I	1479	ENSP00000386259:V1479I;ENSP00000380505:V1479I;ENSP00000416578:V1479I;ENSP00000172853:V1479I	ENSP00000172853:V1479I	V	-	1	0	NEB	152235854	0.007000	0.16637	1.000000	0.80357	0.802000	0.45316	0.019000	0.13444	0.997000	0.38969	-0.254000	0.11334	GTC	C|0.705;T|0.295	0.295	strong		0.483	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543	
FBXO18	84893	hgsc.bcm.edu	37	10	5960434	5960434	+	Missense_Mutation	SNP	T	T	C			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr10:5960434T>C	ENST00000362091.4	+	13	2208	c.2093T>C	c.(2092-2094)cTc>cCc	p.L698P	FBXO18_ENST00000397269.3_Missense_Mutation_p.L185P|FBXO18_ENST00000379999.5_Missense_Mutation_p.L749P	NM_001258453.1|NM_178150.2	NP_001245382.1|NP_835363.1	Q8NFZ0	FBX18_HUMAN	F-box protein, helicase, 18	698					DNA catabolic process, endonucleolytic (GO:0000737)|positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902231)|positive regulation of protein phosphorylation (GO:0001934)|response to intra-S DNA damage checkpoint signaling (GO:0072429)	nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)			NS(2)|breast(2)|kidney(2)|large_intestine(16)|lung(9)|ovary(2)|prostate(3)|skin(3)|stomach(1)	40						GTCTTCTATCTCACGCAGGTA	0.567																																					p.L749P		Atlas-SNP	.											.	FBXO18	108	.	0			c.T2246C						PASS	.						129.0	107.0	114.0					10																	5960434		2203	4300	6503	SO:0001583	missense	84893	exon14			TCTATCTCACGCA	AK095343	CCDS7072.1, CCDS7073.1, CCDS73064.1	10p15.1	2004-08-24	2004-06-15		ENSG00000134452	ENSG00000134452		"""F-boxes /  ""other"""""	13620	protein-coding gene	gene with protein product		607222	"""F-box only protein 18"""			10531037, 11956208	Standard	NM_032807		Approved	FBH1, FLJ14590, Fbx18	uc001iit.4	Q8NFZ0	OTTHUMG00000017609	ENST00000362091.4:c.2093T>C	10.37:g.5960434T>C	ENSP00000355415:p.Leu698Pro	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	64	4	0.0625	NM_032807	Q5JVB0|Q5JVB1|Q7Z4Q6|Q7Z4R0|Q8N1P5|Q8N586|Q96E82|Q96K67|Q96SW7|Q9UFB2	Missense_Mutation	SNP	ENST00000362091.4	37	CCDS7072.1	.	.	.	.	.	.	.	.	.	.	T	26.4	4.736778	0.89482	.	.	ENSG00000134452	ENST00000397269;ENST00000362091;ENST00000379999	D;D;D	0.96685	-4.09;-4.09;-4.09	5.88	5.88	0.94601	.	0.000000	0.85682	D	0.000000	D	0.98131	0.9383	M	0.83953	2.67	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.998;0.998	D	0.99094	1.0841	10	0.87932	D	0	-22.7842	15.9978	0.80265	0.0:0.0:0.0:1.0	.	749;698;624	Q8NFZ0-2;Q8NFZ0;Q2TAK1	.;FBX18_HUMAN;.	P	185;698;749	ENSP00000380439:L185P;ENSP00000355415:L698P;ENSP00000369335:L749P	ENSP00000355415:L698P	L	+	2	0	FBXO18	6000440	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	7.130000	0.77235	2.252000	0.74401	0.529000	0.55759	CTC	.	.	none		0.567	FBXO18-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046596.1	NM_032807	
CLEC18A	348174	hgsc.bcm.edu	37	16	69988292	69988292	+	Missense_Mutation	SNP	C	C	T	rs2549089	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr16:69988292C>T	ENST00000288040.6	+	3	459	c.272C>T	c.(271-273)aCc>aTc	p.T91I	CLEC18A_ENST00000393701.2_Missense_Mutation_p.T91I|CLEC18A_ENST00000568461.1_Missense_Mutation_p.T91I|CLEC18A_ENST00000449317.2_Missense_Mutation_p.T91I	NM_001136214.2	NP_001129686.1	A5D8T8	CL18A_HUMAN	C-type lectin domain family 18, member A	91	SCP.					extracellular region (GO:0005576)	carbohydrate binding (GO:0030246)	p.T91I(2)		NS(1)|endometrium(2)|lung(1)|skin(1)	5						CTCTGTGGAACCCCAACCCCG	0.647													.|||	21	0.00419329	0.0159	0.0	5008	,	,		17779	0.0		0.0	False		,,,				2504	0.0				p.T91I		Atlas-SNP	.											CLEC18A,NS,malignant_melanoma,0,2	CLEC18A	9	2	2	Substitution - Missense(2)	NS(1)|skin(1)	c.C272T						scavenged	.						55.0	53.0	54.0					16																	69988292		2198	4300	6498	SO:0001583	missense	348174	exon4			GTGGAACCCCAAC	AF428259	CCDS10886.1	16q22.1	2010-04-27	2009-03-10	2009-03-10		ENSG00000157322		"""C-type lectin domain containing"""	30388	protein-coding gene	gene with protein product	"""mannose receptor-like"""					12975309	Standard	NM_001136214		Approved	MRCL	uc010vlo.3	A5D8T8		ENST00000288040.6:c.272C>T	16.37:g.69988292C>T	ENSP00000288040:p.Thr91Ile	Somatic	275	0	0		WXS	Illumina HiSeq	Phase_I	288	4	0.0138889	NM_001271197	A8K1G9|Q6DCB3|Q7Z5K9|Q96HH2	Missense_Mutation	SNP	ENST00000288040.6	37	CCDS10886.1	.	.	.	.	.	.	.	.	.	.	.	3.377	-0.127284	0.06753	.	.	ENSG00000157322	ENST00000393701;ENST00000539957;ENST00000449317;ENST00000288040	T;T;T	0.07800	3.16;3.16;3.16	1.97	0.987	0.19790	CAP domain (3);	0.641843	0.13978	N	0.349648	T	0.05227	0.0139	N	0.22421	0.69	0.09310	N	1	B;B;B	0.28470	0.027;0.213;0.078	B;B;B	0.32022	0.014;0.139;0.087	T	0.42816	-0.9429	9	.	.	.	.	4.4066	0.11413	0.0:0.7949:0.0:0.2051	rs2549089	91;91;91	B4DPF2;A5D8T8;F8W692	.;CL18A_HUMAN;.	I	91	ENSP00000377304:T91I;ENSP00000413990:T91I;ENSP00000288040:T91I	.	T	+	2	0	CLEC18A	68545793	0.037000	0.19845	0.022000	0.16811	0.346000	0.29079	0.463000	0.21972	0.390000	0.25115	0.184000	0.17185	ACC	.	.	weak		0.647	CLEC18A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000268955.2	NM_182619	
PLA2G4F	255189	hgsc.bcm.edu	37	15	42434254	42434254	+	Silent	SNP	G	G	A	rs655427	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr15:42434254G>A	ENST00000382396.4	-	20	2564	c.2478C>T	c.(2476-2478)aaC>aaT	p.N826N	PLA2G4F_ENST00000397272.3_Silent_p.N828N			Q68DD2	PA24F_HUMAN	phospholipase A2, group IVF	826	PLA2c. {ECO:0000255|PROSITE- ProRule:PRU00555}.				arachidonic acid secretion (GO:0050482)|cellular response to antibiotic (GO:0071236)|cellular response to organic cyclic compound (GO:0071407)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid catabolic process (GO:0009395)|phospholipid metabolic process (GO:0006644)|prostaglandin biosynthetic process (GO:0001516)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|lysosome (GO:0005764)|ruffle membrane (GO:0032587)|vesicle (GO:0031982)	calcium-dependent phospholipase A2 activity (GO:0047498)|lysophospholipase activity (GO:0004622)|metal ion binding (GO:0046872)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(3)|liver(1)|lung(12)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	32		all_cancers(109;4.82e-12)|all_epithelial(112;5.64e-11)|Lung NSC(122;2.17e-07)|all_lung(180;8.79e-07)|Melanoma(134;0.091)		GBM - Glioblastoma multiforme(94;8.97e-07)		AGGTCTCCACGTTGTTCAGGA	0.602													A|||	2000	0.399361	0.3964	0.415	5008	,	,		16500	0.3452		0.5487	False		,,,				2504	0.2945				p.N826N		Atlas-SNP	.											.	PLA2G4F	75	.	0			c.C2478T						PASS	.	A		1819,2587	638.6+/-397.0	370,1079,754	81.0	76.0	77.0		2478	-10.4	0.0	15	dbSNP_83	77	4536,4062	560.1+/-387.5	1203,2130,966	no	coding-synonymous	PLA2G4F	NM_213600.3		1573,3209,1720	AA,AG,GG		47.2435,41.2846,48.8696		826/850	42434254	6355,6649	2203	4299	6502	SO:0001819	synonymous_variant	255189	exon20			CTCCACGTTGTTC		CCDS32204.1	15q15.1	2008-09-19				ENSG00000168907	3.1.1.4		27396	protein-coding gene	gene with protein product						14702039, 15866882	Standard	NM_213600		Approved	PLA2G4F/Z	uc001zoz.3	Q68DD2		ENST00000382396.4:c.2478C>T	15.37:g.42434254G>A		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	95	6	0.0631579	NM_213600	Q6ZMC8	Silent	SNP	ENST00000382396.4	37	CCDS32204.1																																																																																			G|0.540;N|0.000	.	strong		0.602	PLA2G4F-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000420463.1	NM_213600	
ADPRH	141	hgsc.bcm.edu	37	3	119305379	119305379	+	Silent	SNP	T	T	A	rs25676	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr3:119305379T>A	ENST00000478399.1	+	3	1951	c.546T>A	c.(544-546)gcT>gcA	p.A182A	ADPRH_ENST00000471850.1_3'UTR|ADPRH_ENST00000357003.3_Silent_p.A182A|ADPRH_ENST00000465513.1_Silent_p.A182A|ADPRH_ENST00000478927.1_Silent_p.A182A			P54922	ADPRH_HUMAN	ADP-ribosylarginine hydrolase	182					cellular protein modification process (GO:0006464)|protein de-ADP-ribosylation (GO:0051725)		ADP-ribosylarginine hydrolase activity (GO:0003875)|magnesium ion binding (GO:0000287)			breast(1)|kidney(1)|lung(10)|ovary(1)	13		Lung NSC(201;0.0977)		GBM - Glioblastoma multiforme(114;0.23)		CAGCCTATGCTGTGAATAGCA	0.512													T|||	2065	0.41234	0.4372	0.281	5008	,	,		19874	0.5089		0.2634	False		,,,				2504	0.5256				p.A182A	GBM(133;579 1804 5989 9967 40052)	Atlas-SNP	.											.	ADPRH	33	.	0			c.T546A						PASS	.	T		1754,2652	521.9+/-370.6	359,1036,808	103.0	106.0	105.0		546	-1.0	1.0	3	dbSNP_72	105	2533,6067	414.2+/-351.4	379,1775,2146	no	coding-synonymous	ADPRH	NM_001125.2		738,2811,2954	AA,AT,TT		29.4535,39.8094,32.9617		182/358	119305379	4287,8719	2203	4300	6503	SO:0001819	synonymous_variant	141	exon4			CTATGCTGTGAAT	L13291	CCDS2990.1	3q13.31-q13.33	2004-02-27			ENSG00000144843	ENSG00000144843			269	protein-coding gene	gene with protein product		603081				8349667, 12070318	Standard	NM_001125		Approved	ARH1	uc003ecs.3	P54922	OTTHUMG00000159420	ENST00000478399.1:c.546T>A	3.37:g.119305379T>A		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	68	6	0.0882353	NM_001125	B2R8H1|D3DN83	Silent	SNP	ENST00000478399.1	37	CCDS2990.1																																																																																			T|0.650;A|0.350	0.350	strong		0.512	ADPRH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355199.1	NM_001125	
SH3RF2	153769	hgsc.bcm.edu	37	5	145393364	145393364	+	Missense_Mutation	SNP	C	C	T	rs758037	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr5:145393364C>T	ENST00000511217.1	+	4	851	c.799C>T	c.(799-801)Cgc>Tgc	p.R267C	SH3RF2_ENST00000359120.4_Missense_Mutation_p.R267C			Q8TEC5	SH3R2_HUMAN	SH3 domain containing ring finger 2	267			R -> C (in dbSNP:rs758037). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		negative regulation of phosphatase activity (GO:0010923)|protein ubiquitination (GO:0016567)		ligase activity (GO:0016874)|phosphatase binding (GO:0019902)|protein phosphatase 1 binding (GO:0008157)|protein phosphatase inhibitor activity (GO:0004864)|zinc ion binding (GO:0008270)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|lung(9)|ovary(1)|prostate(1)|skin(2)|stomach(1)	22			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			CCAGTCATCCCGCACAAAAAA	0.527													C|||	3050	0.609026	0.3986	0.5692	5008	,	,		21429	0.7212		0.6312	False		,,,				2504	0.7832				p.R267C		Atlas-SNP	.											.	SH3RF2	58	.	0			c.C799T						PASS	.	C	CYS/ARG	1926,2480	548.2+/-377.5	403,1120,680	81.0	72.0	75.0		799	1.2	0.0	5	dbSNP_86	75	5245,3355	642.9+/-399.9	1604,2037,659	yes	missense	SH3RF2	NM_152550.3	180	2007,3157,1339	TT,TC,CC		39.0116,43.7131,44.8639	probably-damaging	267/730	145393364	7171,5835	2203	4300	6503	SO:0001583	missense	153769	exon5			TCATCCCGCACAA	AL833297	CCDS4280.1	5q32	2013-01-09	2011-11-04	2011-11-04	ENSG00000156463	ENSG00000156463		"""RING-type (C3HC4) zinc fingers"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	26299	protein-coding gene	gene with protein product	"""heart protein phosphatase 1-binding protein"", ""POSH-eliminating RING protein"""	613377	"""protein phosphatase 1, regulatory subunit 39"""	PPP1R39		22128169	Standard	NM_152550		Approved	FLJ23654, RNF158, Hepp1, POSHER	uc003lnt.3	Q8TEC5	OTTHUMG00000129685	ENST00000511217.1:c.799C>T	5.37:g.145393364C>T	ENSP00000424497:p.Arg267Cys	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	120	6	0.05	NM_152550	A8K961|Q08AM9|Q6GMR9|Q8N5S8|Q96LP8	Missense_Mutation	SNP	ENST00000511217.1	37	CCDS4280.1	1340	0.6135531135531136	218	0.44308943089430897	221	0.6104972375690608	406	0.7097902097902098	495	0.6530343007915568	C	10.01	1.233918	0.22626	0.437131	0.609884	ENSG00000156463	ENST00000359120;ENST00000511217	T;T	0.04654	3.58;3.58	5.32	1.22	0.21188	Src homology-3 domain (1);	0.630714	0.16224	N	0.223914	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B	0.11235	0.004	B	0.01281	0.0	T	0.06391	-1.0829	9	0.54805	T	0.06	-1.4343	5.6818	0.17780	0.3218:0.5332:0.0:0.1451	rs758037;rs3733938;rs52807951;rs57396297;rs758037	267	Q8TEC5	SH3R2_HUMAN	C	267	ENSP00000352028:R267C;ENSP00000424497:R267C	ENSP00000352028:R267C	R	+	1	0	SH3RF2	145373557	0.001000	0.12720	0.001000	0.08648	0.671000	0.39405	0.651000	0.24873	-0.025000	0.13918	-0.230000	0.12252	CGC	C|0.411;T|0.589	0.589	strong		0.527	SH3RF2-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372804.1	NM_152550	
MUC4	4585	hgsc.bcm.edu	37	3	195510133	195510133	+	Missense_Mutation	SNP	T	T	C	rs371587475		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr3:195510133T>C	ENST00000463781.3	-	2	8777	c.8318A>G	c.(8317-8319)aAc>aGc	p.N2773S	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.N2773S	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.N2773S(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)		TGAGGAAGTGTTGGTGACAGG	0.582																																					p.N2773S		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,3	MUC4	1505	3	1	Substitution - Missense(1)	kidney(1)	c.A8318G						scavenged	.						42.0	25.0	30.0					3																	195510133		688	1543	2231	SO:0001583	missense	4585	exon2			GAAGTGTTGGTGA	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.8318A>G	3.37:g.195510133T>C	ENSP00000417498:p.Asn2773Ser	Somatic	54	3	0.0555556		WXS	Illumina HiSeq	Phase_I	65	5	0.0769231	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	.	.	.	.	.	.	.	.	.	.	-	0.344	-0.948616	0.02304	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.32753	1.5;1.44	1.02	-1.52	0.08637	.	.	.	.	.	T	0.10465	0.0256	N	0.03608	-0.345	0.09310	N	1	B	0.10296	0.003	B	0.04013	0.001	T	0.32929	-0.9888	8	.	.	.	.	4.3758	0.11270	0.0:0.4779:0.0:0.5221	.	2645	E7ESK3	.	S	2773	ENSP00000417498:N2773S;ENSP00000420243:N2773S	.	N	-	2	0	MUC4	196994912	0.000000	0.05858	0.002000	0.10522	0.016000	0.09150	-4.761000	0.00189	-0.419000	0.07439	0.063000	0.15292	AAC	.	.	weak		0.582	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
MYOM1	8736	hgsc.bcm.edu	37	18	3075746	3075746	+	Silent	SNP	G	G	A	rs1143657	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr18:3075746G>A	ENST00000356443.4	-	35	4995	c.4662C>T	c.(4660-4662)gcC>gcT	p.A1554A	MYOM1_ENST00000400569.3_Silent_p.A1554A|MYOM1_ENST00000261606.7_Silent_p.A1458A	NM_003803.3|NM_019856.1	NP_003794.3|NP_062830.1	P52179	MYOM1_HUMAN	myomesin 1	1554					muscle contraction (GO:0006936)	M band (GO:0031430)|striated muscle myosin thick filament (GO:0005863)	identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|structural constituent of muscle (GO:0008307)	p.A1554A(3)		NS(2)|autonomic_ganglia(1)|central_nervous_system(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(20)|ovary(4)|pancreas(1)|prostate(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	77						ATTCAGCATAGGCCTCATCGT	0.443													G|||	919	0.183506	0.1747	0.183	5008	,	,		18427	0.1875		0.2008	False		,,,				2504	0.1738				p.A1554A		Atlas-SNP	.											MYOM1,NS,carcinoma,0,2	MYOM1	192	2	3	Substitution - coding silent(3)	prostate(2)|stomach(1)	c.C4662T						scavenged	.	G	,	525,3227		38,449,1389	58.0	58.0	58.0		4662,4374	4.2	1.0	18	dbSNP_123	58	1395,6825		108,1179,2823	no	coding-synonymous,coding-synonymous	MYOM1	NM_003803.3,NM_019856.1	,	146,1628,4212	AA,AG,GG		16.9708,13.9925,16.0374	,	1554/1686,1458/1590	3075746	1920,10052	1876	4110	5986	SO:0001819	synonymous_variant	8736	exon35			AGCATAGGCCTCA	AF185573	CCDS45823.1, CCDS45824.1	18p11.31	2014-09-17	2012-10-17		ENSG00000101605	ENSG00000101605		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	7613	protein-coding gene	gene with protein product	"""skelemin"""	603508	"""myomesin 1 (skelemin) (185kD)"", ""myomesin 1 (skelemin) 185kDa"", ""myomesin 1, 185kDa"""			9806852	Standard	NM_019856		Approved		uc002klp.3	P52179	OTTHUMG00000178209	ENST00000356443.4:c.4662C>T	18.37:g.3075746G>A		Somatic	90	1	0.0111111		WXS	Illumina HiSeq	Phase_I	90	4	0.0444444	NM_003803	Q14BD6|Q6H969|Q6ZUU0	Silent	SNP	ENST00000356443.4	37	CCDS45824.1																																																																																			G|0.810;A|0.190	0.190	strong		0.443	MYOM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441037.2	NM_003803	
UGT2B11	10720	hgsc.bcm.edu	37	4	70070366	70070366	+	Splice_Site	SNP	A	A	T	rs144106768	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr4:70070366A>T	ENST00000446444.1	-	5	1100	c.1092T>A	c.(1090-1092)ggT>ggA	p.G364G	RP11-704M14.1_ENST00000505646.1_RNA|RP11-704M14.1_ENST00000504301.1_RNA	NM_001073.1	NP_001064.1	O75310	UDB11_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide B11	364					estrogen metabolic process (GO:0008210)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	glucuronosyltransferase activity (GO:0015020)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(18)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	42						TTTTTGGATGACCTAGGATTG	0.378													.|||	272	0.0543131	0.0408	0.0115	5008	,	,		19330	0.1885		0.004	False		,,,				2504	0.0164				p.G364G		Atlas-SNP	.											.	UGT2B11	92	.	0			c.T1092A						PASS	.	A		111,4059		1,109,1975	37.0	40.0	39.0		1092	2.0	1.0	4	dbSNP_134	39	2,8182		0,2,4090	no	coding-synonymous-near-splice	UGT2B11	NM_001073.1		1,111,6065	TT,TA,AA		0.0244,2.6619,0.9147		364/530	70070366	113,12241	2085	4092	6177	SO:0001630	splice_region_variant	10720	exon5			TGGATGACCTAGG	AF016492	CCDS3527.1	4q13.3	2008-02-05	2005-07-20		ENSG00000213759	ENSG00000213759		"""UDP glucuronosyltransferases"""	12545	protein-coding gene	gene with protein product		603064	"""UDP glycosyltransferase 2 family, polypeptide B11"""			9675083	Standard	NM_001073		Approved		uc003heh.3	O75310	OTTHUMG00000129395	ENST00000446444.1:c.1091-1T>A	4.37:g.70070366A>T		Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	161	11	0.068323	NM_001073	Q3KNV9	Silent	SNP	ENST00000446444.1	37	CCDS3527.1																																																																																			.	.	weak		0.378	UGT2B11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251551.2	NM_001073	Silent
UBAP2	55833	hgsc.bcm.edu	37	9	33941759	33941759	+	Missense_Mutation	SNP	T	T	C	rs307658	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr9:33941759T>C	ENST00000379238.1	-	16	1934	c.1817A>G	c.(1816-1818)aAt>aGt	p.N606S	UBAP2_ENST00000379225.1_Missense_Mutation_p.N239S|UBAP2_ENST00000539807.1_Missense_Mutation_p.N361S|UBAP2_ENST00000379239.4_Missense_Mutation_p.N339S|UBAP2_ENST00000449054.1_Missense_Mutation_p.N606S|UBAP2_ENST00000418786.2_Missense_Mutation_p.N553S|UBAP2_ENST00000360802.1_Missense_Mutation_p.N606S					ubiquitin associated protein 2									p.N606S(1)		endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(13)|ovary(3)|stomach(1)	32			LUSC - Lung squamous cell carcinoma(29;0.00575)	GBM - Glioblastoma multiforme(74;0.168)		ACTAGCAGAATTCAGTGATGA	0.448													C|||	1857	0.370807	0.5083	0.268	5008	,	,		18167	0.1726		0.3837	False		,,,				2504	0.4489				p.N606S		Atlas-SNP	.											UBAP2,NS,carcinoma,0,1	UBAP2	82	1	1	Substitution - Missense(1)	stomach(1)	c.A1817G						scavenged	.	C	SER/ASN	2060,2346	607.3+/-390.9	478,1104,621	174.0	159.0	164.0		1817	5.8	1.0	9	dbSNP_79	164	3291,5309	646.8+/-400.3	648,1995,1657	yes	missense	UBAP2	NM_018449.2	46	1126,3099,2278	CC,CT,TT		38.2674,46.7544,41.1425	benign	606/1120	33941759	5351,7655	2203	4300	6503	SO:0001583	missense	55833	exon16			GCAGAATTCAGTG	AB040924	CCDS6547.1, CCDS75828.1	9p11.2	2008-02-05			ENSG00000137073	ENSG00000137073			14185	protein-coding gene	gene with protein product						8871400	Standard	NM_018449		Approved	KIAA1491, bA176F3.5, FLJ22435	uc003ztq.1	Q5T6F2	OTTHUMG00000000427	ENST00000379238.1:c.1817A>G	9.37:g.33941759T>C	ENSP00000368540:p.Asn606Ser	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	107	4	0.0373832	NM_018449		Missense_Mutation	SNP	ENST00000379238.1	37	CCDS6547.1	778	0.35622710622710624	248	0.5040650406504065	106	0.292817679558011	114	0.1993006993006993	310	0.40897097625329815	C	1.094	-0.663234	0.03428	0.467544	0.382674	ENSG00000137073	ENST00000379238;ENST00000449054;ENST00000360802;ENST00000431417;ENST00000379239;ENST00000539807;ENST00000418786;ENST00000379225	T;T;T;T;T;T;T	0.20738	2.79;2.79;2.79;2.58;2.59;2.28;2.05	5.76	5.76	0.90799	.	0.521330	0.23587	N	0.046596	T	0.00012	0.0000	N	0.01015	-1.05	0.58432	P	4.000000000004E-6	B;B;B;B;B;B;B;B	0.17038	0.0;0.006;0.0;0.0;0.0;0.001;0.003;0.02	B;B;B;B;B;B;B;B	0.06405	0.001;0.0;0.0;0.0;0.0;0.0;0.0;0.002	T	0.41124	-0.9526	9	0.02654	T	1	-4.2248	12.9291	0.58276	0.0:0.866:0.0:0.134	rs307658;rs601694;rs1626808;rs52833981;rs60695207;rs307658	553;531;361;339;515;239;531;606	E7EWG4;F5H4D5;F5H2U4;A6NCA8;F5H2C8;A2A306;B4DH66;Q5T6F2	.;.;.;.;.;.;.;UBAP2_HUMAN	S	606;606;606;515;339;361;553;239	ENSP00000368540:N606S;ENSP00000416932:N606S;ENSP00000354039:N606S;ENSP00000368541:N339S;ENSP00000439329:N361S;ENSP00000404436:N553S;ENSP00000368527:N239S	ENSP00000354039:N606S	N	-	2	0	UBAP2	33931759	1.000000	0.71417	1.000000	0.80357	0.356000	0.29392	2.117000	0.41939	1.449000	0.47699	-0.119000	0.15052	AAT	T|0.617;C|0.383	0.383	strong		0.448	UBAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001071.1	NM_018449	
DNAH8	1769	hgsc.bcm.edu	37	6	38781866	38781866	+	Silent	SNP	C	C	G	rs1678690	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr6:38781866C>G	ENST00000359357.3	+	23	2897	c.2643C>G	c.(2641-2643)tcC>tcG	p.S881S	DNAH8_ENST00000449981.2_Silent_p.S1098S|DNAH8_ENST00000441566.1_Silent_p.S881S			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8	881					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)	p.S881S(1)		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						ATATTATTTCCTTTATAAAAA	0.313													C|||	2510	0.501198	0.3124	0.5908	5008	,	,		18086	0.7946		0.3748	False		,,,				2504	0.5204				p.S1098S		Atlas-SNP	.											DNAH8_ENST00000359357,NS,carcinoma,0,1	DNAH8	1239	1	1	Substitution - coding silent(1)	prostate(1)	c.C3294G						scavenged	.	C		1493,2913	473.1+/-356.6	252,989,962	115.0	127.0	123.0		3294	2.1	1.0	6	dbSNP_89	123	3726,4874	529.8+/-381.7	823,2080,1397	no	coding-synonymous	DNAH8	NM_001206927.1		1075,3069,2359	GG,GC,CC		43.3256,33.8856,40.1276		1098/4708	38781866	5219,7787	2203	4300	6503	SO:0001819	synonymous_variant	1769	exon25			TATTTCCTTTATA	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.2643C>G	6.37:g.38781866C>G		Somatic	276	1	0.00362319		WXS	Illumina HiSeq	Phase_I	257	6	0.0233463	NM_001206927	O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	Silent	SNP	ENST00000359357.3	37																																																																																				C|0.558;G|0.442	0.442	strong		0.313	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043574.1	NM_001206927	
FLG2	388698	hgsc.bcm.edu	37	1	152328051	152328051	+	Silent	SNP	T	T	C			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr1:152328051T>C	ENST00000388718.5	-	3	2283	c.2211A>G	c.(2209-2211)tcA>tcG	p.S737S	FLG-AS1_ENST00000392688.2_RNA|FLG-AS1_ENST00000445097.1_RNA	NM_001014342.2	NP_001014364.1	Q5D862	FILA2_HUMAN	filaggrin family member 2	737	Ser-rich.				establishment of skin barrier (GO:0061436)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			NS(2)|breast(7)|cervix(3)|endometrium(11)|kidney(9)|large_intestine(24)|liver(1)|lung(85)|ovary(12)|pancreas(1)|prostate(6)|skin(17)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	188	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			GACCTGAGCCTGATCCATGTT	0.502																																					p.S737S		Atlas-SNP	.											FLG2,NS,carcinoma,-1,1	FLG2	431	1	0			c.A2211G						scavenged	.						313.0	309.0	310.0					1																	152328051		2203	4300	6503	SO:0001819	synonymous_variant	388698	exon3			TGAGCCTGATCCA	AY827490	CCDS30861.1	1q21.3	2013-01-10			ENSG00000143520	ENSG00000143520		"""EF-hand domain containing"""	33276	protein-coding gene	gene with protein product						12477932	Standard	NM_001014342		Approved	IFPS	uc001ezw.4	Q5D862	OTTHUMG00000012245	ENST00000388718.5:c.2211A>G	1.37:g.152328051T>C		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	191	6	0.0314136	NM_001014342	Q9H4U1	Silent	SNP	ENST00000388718.5	37	CCDS30861.1																																																																																			.	.	none		0.502	FLG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034018.5	NM_001014342	
SHISA2	387914	hgsc.bcm.edu	37	13	26620924	26620924	+	Silent	SNP	G	G	A	rs77010561	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr13:26620924G>A	ENST00000319420.3	-	2	670	c.615C>T	c.(613-615)aaC>aaT	p.N205N		NM_001007538.1	NP_001007539.1	Q6UWI4	SHSA2_HUMAN	shisa family member 2	205					multicellular organismal development (GO:0007275)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(7)|ovary(1)|prostate(2)|skin(1)	17						GCAAGCAACAGTTGGTCTGTG	0.607													G|||	553	0.110423	0.0817	0.0605	5008	,	,		20279	0.2351		0.0	False		,,,				2504	0.1697				p.N205N		Atlas-SNP	.											.	SHISA2	43	.	0			c.C615T						PASS	.	G		266,4140	151.4+/-185.3	9,248,1946	128.0	123.0	125.0		615	4.4	1.0	13	dbSNP_131	125	5,8595	5.0+/-18.6	0,5,4295	no	coding-synonymous	SHISA2	NM_001007538.1		9,253,6241	AA,AG,GG		0.0581,6.0372,2.0837		205/296	26620924	271,12735	2203	4300	6503	SO:0001819	synonymous_variant	387914	exon2			GCAACAGTTGGTC		CCDS31951.1	13q12.13	2013-07-31	2013-07-31	2008-04-01	ENSG00000180730	ENSG00000180730		"""Shisa homologs"""	20366	protein-coding gene	gene with protein product			"""chromosome 13 open reading frame 13"", ""transmembrane protein 46"", ""shisa homolog 2 (Xenopus laevis)"""	C13orf13, TMEM46			Standard	NM_001007538		Approved	bA398O19.2, PRO28631, WGAR9166, hShisa	uc001uqm.1	Q6UWI4	OTTHUMG00000016612	ENST00000319420.3:c.615C>T	13.37:g.26620924G>A		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	94	5	0.0531915	NM_001007538	B9EH70|Q5W0G8	Silent	SNP	ENST00000319420.3	37	CCDS31951.1																																																																																			G|0.962;A|0.038	0.038	strong		0.607	SHISA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044239.2	NM_001007538	
ZNF658	26149	hgsc.bcm.edu	37	9	40773337	40773337	+	Silent	SNP	C	C	T	rs78487056	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr9:40773337C>T	ENST00000602553.1	-	5	2232	c.1938G>A	c.(1936-1938)aaG>aaA	p.K646K	ZNF658_ENST00000441795.1_Intron|ZNF658_ENST00000377626.3_Silent_p.K646K			Q5TYW1	ZN658_HUMAN	zinc finger protein 658	646					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)	p.K646K(1)		breast(3)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(9)|lung(21)|ovary(2)|prostate(1)|upper_aerodigestive_tract(2)	46				GBM - Glioblastoma multiforme(29;0.02)|Lung(182;0.0681)		TTTGATGTGCCTTGAGAACAG	0.418													C|||	1047	0.209065	0.0424	0.2478	5008	,	,		19384	0.3482		0.2217	False		,,,				2504	0.2505				p.K646K		Atlas-SNP	.											ZNF658,NS,carcinoma,0,1	ZNF658	100	1	1	Substitution - coding silent(1)	ovary(1)	c.G1938A						scavenged	.	C		300,4104	158.9+/-191.5	20,260,1922	120.0	128.0	125.0		1938	-2.4	0.0	9	dbSNP_131	125	1790,6806	315.5+/-312.3	172,1446,2680	no	coding-synonymous	ZNF658	NM_033160.5		192,1706,4602	TT,TC,CC		20.8236,6.812,16.0769		646/1060	40773337	2090,10910	2202	4298	6500	SO:0001819	synonymous_variant	26149	exon5			ATGTGCCTTGAGA	AA482262	CCDS75846.1	9p13.1	2013-01-08			ENSG00000196409	ENSG00000274349		"""Zinc fingers, C2H2-type"", ""-"""	25226	protein-coding gene	gene with protein product							Standard	NM_033160		Approved	MGC35232, DKFZp572C163, FLJ32813	uc004abs.2	Q5TYW1	OTTHUMG00000013392	ENST00000602553.1:c.1938G>A	9.37:g.40773337C>T		Somatic	216	0	0		WXS	Illumina HiSeq	Phase_I	176	4	0.0227273	NM_033160	Q6PIP3|Q96M55|Q9H9S6|Q9UG02	Silent	SNP	ENST00000602553.1	37	CCDS35023.1																																																																																			C|0.824;T|0.176	0.176	strong		0.418	ZNF658-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467800.1	NM_033160	
SETD6	79918	hgsc.bcm.edu	37	16	58550484	58550484	+	Silent	SNP	G	G	A	rs3743567	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr16:58550484G>A	ENST00000219315.4	+	4	629	c.579G>A	c.(577-579)ctG>ctA	p.L193L	SETD6_ENST00000418480.1_3'UTR|SETD6_ENST00000310682.2_Silent_p.L169L|SETD6_ENST00000394266.4_Intron			Q8TBK2	SETD6_HUMAN	SET domain containing 6	193	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				negative regulation of NF-kappaB transcription factor activity (GO:0032088)|peptidyl-lysine monomethylation (GO:0018026)|regulation of inflammatory response (GO:0050727)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	NF-kappaB binding (GO:0051059)|protein-lysine N-methyltransferase activity (GO:0016279)			endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)|skin(1)	7						CCATCGTGCTGCCCTTCATGG	0.617													G|||	691	0.137979	0.0953	0.1182	5008	,	,		16684	0.1796		0.0795	False		,,,				2504	0.227				p.L193L		Atlas-SNP	.											.	SETD6	27	.	0			c.G579A						PASS	.	G	,	401,3995	199.8+/-223.2	17,367,1814	104.0	109.0	107.0		579,507	2.3	1.0	16	dbSNP_107	107	825,7775	190.7+/-237.1	39,747,3514	no	coding-synonymous,coding-synonymous	SETD6	NM_001160305.1,NM_024860.2	,	56,1114,5328	AA,AG,GG		9.593,9.1219,9.4337	,	193/474,169/450	58550484	1226,11770	2198	4300	6498	SO:0001819	synonymous_variant	79918	exon4			CGTGCTGCCCTTC	AK024801	CCDS10798.1, CCDS54013.1	16q21	2008-02-05			ENSG00000103037	ENSG00000103037			26116	protein-coding gene	gene with protein product						12477932	Standard	NM_024860		Approved	FLJ21148	uc002ens.3	Q8TBK2	OTTHUMG00000150276	ENST00000219315.4:c.579G>A	16.37:g.58550484G>A		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	89	5	0.0561798	NM_001160305	A8K380|B5ME38|Q9H787	Silent	SNP	ENST00000219315.4	37	CCDS54013.1																																																																																			G|0.896;A|0.104	0.104	strong		0.617	SETD6-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000317274.2	NM_024860	
SIRPB1	10326	hgsc.bcm.edu	37	20	1592120	1592120	+	Intron	SNP	G	G	T	rs1135201		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr20:1592120G>T	ENST00000381605.4	-	1	141				SIRPB1_ENST00000381603.3_Intron|SIRPB1_ENST00000568365.1_Missense_Mutation_p.R106S|SIRPB1_ENST00000279477.7_Missense_Mutation_p.R106S|SIRPB1_ENST00000381596.1_5'UTR|RP4-576H24.4_ENST00000564763.1_Intron	NM_006065.3	NP_006056.2	O00241	SIRB1_HUMAN	signal-regulatory protein beta 1						cell surface receptor signaling pathway (GO:0007166)|innate immune response (GO:0045087)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				central_nervous_system(2)|kidney(2)|large_intestine(4)|lung(16)|ovary(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)	31						TTACTGATGCGGATGGAAAAG	0.512																																					p.R106S		Atlas-SNP	.											SIRPB1_ENST00000279477,NS,carcinoma,0,1	SIRPB1	83	1	0			c.C316A						scavenged	.						105.0	121.0	117.0					20																	1592120		448	1337	1785	SO:0001627	intron_variant	10326	exon2			TGATGCGGATGGA	Y10376	CCDS13019.1, CCDS42850.1, CCDS46571.1	20p13	2013-01-11			ENSG00000101307	ENSG00000101307		"""Signal-regulatory proteins"", ""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C1-set domain containing"""	15928	protein-coding gene	gene with protein product		603889				9062191, 16339511	Standard	NM_001083910		Approved	SIRP-BETA-1, CD172b	uc010gai.3	O00241	OTTHUMG00000031676	ENST00000381605.4:c.76+8394C>A	20.37:g.1592120G>T		Somatic	139	5	0.0359712		WXS	Illumina HiSeq	Phase_I	134	6	0.0447761	NM_001135844	A6NLM2|B2R8V0|Q5TFQ9|Q5TFR0|Q8TB12|Q9H1U5|Q9Y4V0	Missense_Mutation	SNP	ENST00000381605.4	37	CCDS13019.1	560	0.2564102564102564	150	0.3048780487804878	74	0.20441988950276244	183	0.31993006993006995	153	0.20184696569920843	.	2.402	-0.337253	0.05278	.	.	ENSG00000101307	ENST00000279477;ENST00000381596	T	0.65364	-0.15	2.65	-2.79	0.05841	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00012	0.0000	L	0.52266	1.64	0.34870	D	0.743495	B	0.31435	0.323	B	0.31869	0.137	T	0.37753	-0.9692	9	0.37606	T	0.19	.	4.2858	0.10855	0.1304:0.0:0.2968:0.5727	rs1135201;rs3197735	106	Q5TFQ8	SIRBL_HUMAN	S	106	ENSP00000279477:R106S	ENSP00000279477:R106S	R	-	1	0	SIRPB1	1540120	0.081000	0.21417	0.142000	0.22268	0.020000	0.10135	0.000000	0.12993	-0.294000	0.08973	-2.062000	0.00397	CGC	G|0.744;T|0.256	0.256	strong		0.512	SIRPB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077555.2	NM_006065	
USP32	84669	hgsc.bcm.edu	37	17	58275693	58275693	+	Missense_Mutation	SNP	G	G	T	rs202121527		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr17:58275693G>T	ENST00000300896.4	-	27	3556	c.3362C>A	c.(3361-3363)gCg>gAg	p.A1121E	USP32_ENST00000592339.1_Missense_Mutation_p.A791E	NM_032582.3	NP_115971.2	Q8NFA0	UBP32_HUMAN	ubiquitin specific peptidase 32	1121	USP.				protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)	Golgi apparatus (GO:0005794)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)	p.A1121V(1)		NS(3)|breast(5)|endometrium(5)|kidney(4)|large_intestine(12)|liver(1)|lung(24)|pancreas(1)|prostate(3)|skin(3)|urinary_tract(1)	62	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;2.02e-11)|all cancers(12;5.23e-10)|Colorectal(3;0.198)			AATCCAAACCGCATCATATAG	0.488																																					p.A1121E		Atlas-SNP	.											USP32,rectum,carcinoma,0,3	USP32	128	3	1	Substitution - Missense(1)	large_intestine(1)	c.C3362A						scavenged	.						176.0	157.0	163.0					17																	58275693		2203	4300	6503	SO:0001583	missense	84669	exon27			CAAACCGCATCAT	AF533230	CCDS32697.1	17q23.3	2013-01-10	2005-08-08		ENSG00000170832	ENSG00000170832		"""Ubiquitin-specific peptidases"", ""EF-hand domain containing"""	19143	protein-coding gene	gene with protein product		607740	"""ubiquitin specific protease 32"""			12838346	Standard	NM_032582		Approved	NY-REN-60, USP10	uc002iyo.1	Q8NFA0		ENST00000300896.4:c.3362C>A	17.37:g.58275693G>T	ENSP00000300896:p.Ala1121Glu	Somatic	234	0	0		WXS	Illumina HiSeq	Phase_I	243	3	0.0123457	NM_032582	Q7Z5T3|Q9BX85|Q9Y591	Missense_Mutation	SNP	ENST00000300896.4	37	CCDS32697.1	.	.	.	.	.	.	.	.	.	.	G	22.9	4.348378	0.82132	.	.	ENSG00000170832	ENST00000300896	T	0.45668	0.89	5.15	5.15	0.70609	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.000000	0.85682	D	0.000000	T	0.39682	0.1087	L	0.43152	1.355	0.80722	D	1	P	0.35242	0.492	B	0.41174	0.349	T	0.16928	-1.0386	10	0.05525	T	0.97	.	18.6199	0.91317	0.0:0.0:1.0:0.0	.	1121	Q8NFA0	UBP32_HUMAN	E	1121	ENSP00000300896:A1121E	ENSP00000300896:A1121E	A	-	2	0	USP32	55630475	1.000000	0.71417	0.992000	0.48379	0.970000	0.65996	7.963000	0.87922	2.381000	0.81170	0.561000	0.74099	GCG	G|1.000;A|0.000	.	alt		0.488	USP32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449235.2	NM_032582	
ANKRD11	29123	hgsc.bcm.edu	37	16	89352567	89352567	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr16:89352567C>T	ENST00000301030.4	-	8	1232	c.772G>A	c.(772-774)Ggg>Agg	p.G258R	ANKRD11_ENST00000378330.2_Missense_Mutation_p.G258R	NM_001256183.1|NM_013275.5	NP_001243112.1|NP_037407.4	Q6UB99	ANR11_HUMAN	ankyrin repeat domain 11	258					bone development (GO:0060348)|face morphogenesis (GO:0060325)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|odontogenesis of dentin-containing tooth (GO:0042475)|skeletal system morphogenesis (GO:0048705)|tissue homeostasis (GO:0001894)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(4)|central_nervous_system(3)|endometrium(17)|kidney(2)|large_intestine(18)|lung(20)|ovary(6)|pancreas(1)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	83		all_hematologic(23;0.00824)|Colorectal(91;0.0475)		Epithelial(1;5.33e-11)|all cancers(4;2.6e-09)|OV - Ovarian serous cystadenocarcinoma(4;2.29e-07)|BRCA - Breast invasive adenocarcinoma(80;0.0142)		TGCGGGTTCCCTCCGTACCGC	0.582																																					p.G258R		Atlas-SNP	.											.	ANKRD11	195	.	0			c.G772A						PASS	.						122.0	121.0	121.0					16																	89352567		2198	4300	6498	SO:0001583	missense	29123	exon8			GGTTCCCTCCGTA	AY373756	CCDS32513.1	16q24.3	2013-01-10				ENSG00000167522		"""Ankyrin repeat domain containing"""	21316	protein-coding gene	gene with protein product		611192				11483580	Standard	NM_001256182		Approved	LZ16, T13	uc002fnc.2	Q6UB99		ENST00000301030.4:c.772G>A	16.37:g.89352567C>T	ENSP00000301030:p.Gly258Arg	Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	53	19	0.358491	NM_001256183	Q6NTG1|Q6QMF8	Missense_Mutation	SNP	ENST00000301030.4	37	CCDS32513.1	.	.	.	.	.	.	.	.	.	.	C	35	5.557873	0.96514	.	.	ENSG00000167522	ENST00000301030;ENST00000378330;ENST00000378332	T;T	0.65178	-0.14;-0.14	6.11	6.11	0.99139	Ankyrin repeat-containing domain (3);	0.000000	0.85682	D	0.000000	T	0.75133	0.3808	L	0.41906	1.305	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.75068	-0.3448	10	0.87932	D	0	.	20.7342	0.99715	0.0:1.0:0.0:0.0	.	258	Q6UB99	ANR11_HUMAN	R	258;258;272	ENSP00000301030:G258R;ENSP00000367581:G258R	ENSP00000301030:G258R	G	-	1	0	ANKRD11	87880068	1.000000	0.71417	0.756000	0.31282	0.773000	0.43773	7.527000	0.81931	2.906000	0.99361	0.655000	0.94253	GGG	.	.	none		0.582	ANKRD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430462.3	NM_013275	
PRG4	10216	hgsc.bcm.edu	37	1	186276981	186276981	+	Silent	SNP	A	A	G			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr1:186276981A>G	ENST00000445192.2	+	7	2175	c.2130A>G	c.(2128-2130)aaA>aaG	p.K710K	PRG4_ENST00000367484.3_Intron|PRG4_ENST00000367483.4_Silent_p.K669K|PRG4_ENST00000367486.3_Silent_p.K667K|PRG4_ENST00000367485.4_Silent_p.K617K	NM_005807.3	NP_005798.2	Q92954	PRG4_HUMAN	proteoglycan 4	710	59 X 8 AA repeats of K-X-P-X-P-T-T-X.				cell proliferation (GO:0008283)|hematopoietic stem cell proliferation (GO:0071425)|immune response (GO:0006955)|negative regulation of interleukin-6 biosynthetic process (GO:0045409)|regulation of cell proliferation (GO:0042127)	extracellular space (GO:0005615)	polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(33)|prostate(7)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(1)	102						CTACCCCTAAAGGGACTGCTC	0.582																																					p.K710K		Atlas-SNP	.											PRG4,NS,carcinoma,0,6	PRG4	259	6	0			c.A2130G						scavenged	.						162.0	175.0	171.0					1																	186276981		2203	4300	6503	SO:0001819	synonymous_variant	10216	exon7			CCCTAAAGGGACT	U70136	CCDS1369.1, CCDS44287.1, CCDS44288.1	1q25-q31	2008-07-18	2004-11-15		ENSG00000116690	ENSG00000116690			9364	protein-coding gene	gene with protein product	"""lubricin"", ""megakaryocyte stimulating factor"", ""articular superficial zone protein"", ""Jacobs camptodactyly-arthropathy-pericarditis syndrome"", ""camptodactyly, arthropathy, coxa vara, pericarditis syndrome"", ""bG174L6.2 (MSF: megakaryocyte stimulating factor )"""	604283	"""proteoglycan 4, (megakaryocyte stimulating factor, articular superficial zone protein, camptodactyly, arthropathy, coxa vara, pericarditis syndrome)"""	CACP		10545950, 9920774	Standard	NM_005807		Approved	JCAP, SZP, MSF, HAPO, bG174L6.2, FLJ32635	uc001gru.4	Q92954	OTTHUMG00000035574	ENST00000445192.2:c.2130A>G	1.37:g.186276981A>G		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	139	3	0.0215827	NM_005807	Q6DNC4|Q6DNC5|Q6ZMZ5|Q9BX49	Silent	SNP	ENST00000445192.2	37	CCDS1369.1																																																																																			.	.	none		0.582	PRG4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000086346.1	NM_005807	
CFAP69	79846	hgsc.bcm.edu	37	7	89906609	89906609	+	Silent	SNP	C	C	T	rs3761805	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr7:89906609C>T	ENST00000389297.4	+	11	1367	c.1116C>T	c.(1114-1116)aaC>aaT	p.N372N	C7orf63_ENST00000316089.8_Silent_p.N372N|C7orf63_ENST00000497910.1_Silent_p.N354N	NM_001039706.2|NM_001160138.1	NP_001034795.2|NP_001153610.1	A5D8W1	CG063_HUMAN		372										breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(12)|lung(14)|ovary(1)|prostate(3)	37						TACTATTCAACGTAATTGTGA	0.284													T|||	2022	0.403754	0.4206	0.3905	5008	,	,		16063	0.6855		0.2286	False		,,,				2504	0.2802				p.N372N		Atlas-SNP	.											C7orf63_ENST00000389297,colon,carcinoma,+2,2	C7orf63	158	2	0			c.C1116T						scavenged	.	T	,	1262,2320		226,810,755	39.0	41.0	40.0		1116,1062	1.1	1.0	7	dbSNP_107	40	1491,6557		133,1225,2666	no	coding-synonymous,coding-synonymous	C7orf63	NM_001039706.2,NM_001160138.1	,	359,2035,3421	TT,TC,CC		18.5263,35.2317,23.6715	,	372/942,354/924	89906609	2753,8877	1791	4024	5815	SO:0001819	synonymous_variant	79846	exon11			ATTCAACGTAATT																												ENST00000389297.4:c.1116C>T	7.37:g.89906609C>T		Somatic	269	0	0		WXS	Illumina HiSeq	Phase_I	263	8	0.0304183	NM_001039706	A3KMP9|B4DYW6|B4DZP7|B9EIM7|Q6V705|Q8IY89|Q9H7C2	Silent	SNP	ENST00000389297.4	37	CCDS43613.2																																																																																			C|0.602;T|0.398	0.398	strong		0.284	C7orf63-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139891.4		
FBXO30	84085	hgsc.bcm.edu	37	6	146125793	146125793	+	Missense_Mutation	SNP	A	A	T	rs3811102	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr6:146125793A>T	ENST00000237281.4	-	2	1915	c.1749T>A	c.(1747-1749)caT>caA	p.H583Q		NM_032145.4	NP_115521.3	Q8TB52	FBX30_HUMAN	F-box protein 30	583			H -> Q (in dbSNP:rs3811102). {ECO:0000269|Ref.3}.				ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(11)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26		Ovarian(120;0.0776)		OV - Ovarian serous cystadenocarcinoma(155;1.95e-07)|GBM - Glioblastoma multiforme(68;0.0149)		ATGACCTCAAATGGCGGTCAT	0.418																																					p.H583Q		Atlas-SNP	.											.	FBXO30	56	.	0			c.T1749A						PASS	.	A	GLN/HIS	960,3446	362.6+/-316.2	110,740,1353	99.0	86.0	91.0		1749	0.4	0.9	6	dbSNP_107	91	3546,5052	515.7+/-378.7	724,2098,1477	yes	missense	FBXO30	NM_032145.4	24	834,2838,2830	TT,TA,AA		41.2421,21.7885,34.6509	probably-damaging	583/746	146125793	4506,8498	2203	4299	6502	SO:0001583	missense	84085	exon2			CCTCAAATGGCGG	AF248640	CCDS5208.1	6q24	2008-02-05	2004-06-15		ENSG00000118496	ENSG00000118496		"""F-boxes /  ""other"""""	15600	protein-coding gene	gene with protein product		609101	"""F-box only protein, helicase, 18"""				Standard	XM_005267159		Approved	MGC21674, Fbx30	uc003qla.3	Q8TB52	OTTHUMG00000015749	ENST00000237281.4:c.1749T>A	6.37:g.146125793A>T	ENSP00000237281:p.His583Gln	Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	114	6	0.0526316	NM_032145	Q9BXZ7	Missense_Mutation	SNP	ENST00000237281.4	37	CCDS5208.1	654	0.29945054945054944	106	0.21544715447154472	89	0.24585635359116023	149	0.26048951048951047	310	0.40897097625329815	A	9.123	1.009522	0.19277	0.217885	0.412421	ENSG00000118496	ENST00000237281	T	0.17213	2.29	5.73	0.452	0.16634	.	0.135004	0.64402	N	0.000002	T	0.03520	0.0101	L	0.29908	0.895	0.23030	P	0.99840109	B	0.06786	0.001	B	0.12156	0.007	T	0.35375	-0.9791	9	0.46703	T	0.11	-7.8808	5.4721	0.16676	0.5341:0.2505:0.2154:0.0	rs3811102;rs17822232;rs3811102	583	Q8TB52	FBX30_HUMAN	Q	583	ENSP00000237281:H583Q	ENSP00000237281:H583Q	H	-	3	2	FBXO30	146167486	0.953000	0.32496	0.912000	0.35992	0.957000	0.61999	0.282000	0.18829	-0.138000	0.11434	0.533000	0.62120	CAT	A|0.672;T|0.328	0.328	strong		0.418	FBXO30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042570.2		
TYR	7299	hgsc.bcm.edu	37	11	88911368	88911368	+	Missense_Mutation	SNP	G	G	A	rs149684917		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr11:88911368G>A	ENST00000263321.5	+	1	749	c.247G>A	c.(247-249)Gtc>Atc	p.V83I	TYR_ENST00000526139.1_3'UTR	NM_000372.4	NP_000363.1	P14679	TYRO_HUMAN	tyrosinase	83					cell proliferation (GO:0008283)|eye pigment biosynthetic process (GO:0006726)|melanin biosynthetic process from tyrosine (GO:0006583)|thymus development (GO:0048538)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|Golgi-associated vesicle (GO:0005798)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|melanosome (GO:0042470)|perinuclear region of cytoplasm (GO:0048471)	copper ion binding (GO:0005507)|monophenol monooxygenase activity (GO:0004503)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(25)|ovary(2)|pancreas(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	48		Acute lymphoblastic leukemia(157;2.33e-05)|all_hematologic(158;0.0033)			Azelaic Acid(DB00548)|Mimosine(DB01055)|Monobenzone(DB00600)	GTGGCCTTCCGTCTTTTATAA	0.512																																					p.V83I		Atlas-SNP	.											.	TYR	130	.	0			c.G247A						PASS	.	G	ILE/VAL	0,4402		0,0,2201	43.0	42.0	43.0		247	3.2	0.5	11	dbSNP_134	43	1,8597	1.2+/-3.3	0,1,4298	no	missense	TYR	NM_000372.4	29	0,1,6499	AA,AG,GG		0.0116,0.0,0.0077	benign	83/530	88911368	1,12999	2201	4299	6500	SO:0001583	missense	7299	exon1			CCTTCCGTCTTTT	M27160	CCDS8284.1	11q14.3	2013-09-27	2012-09-28		ENSG00000077498	ENSG00000077498	1.14.18.1		12442	protein-coding gene	gene with protein product	"""oculocutaneous albinism IA"""	606933					Standard	NM_000372		Approved	OCAIA, OCA1A, OCA1	uc001pcs.3	P14679	OTTHUMG00000167294	ENST00000263321.5:c.247G>A	11.37:g.88911368G>A	ENSP00000263321:p.Val83Ile	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	64	24	0.375	NM_000372	Q15675|Q15676|Q15680|Q8TAK4|Q9BYY0|Q9BZX1	Missense_Mutation	SNP	ENST00000263321.5	37	CCDS8284.1	.	.	.	.	.	.	.	.	.	.	G	8.247	0.808214	0.16467	0.0	1.16E-4	ENSG00000077498	ENST00000263321	D	0.83591	-1.74	6.07	3.24	0.37175	Uncharacterised domain, di-copper centre (2);	0.232469	0.43919	N	0.000506	D	0.82834	0.5123	M	0.80508	2.5	0.35898	D	0.830158	B	0.21520	0.057	B	0.18561	0.022	T	0.80625	-0.1299	9	.	.	.	.	15.4391	0.75168	0.1263:0.0:0.8737:0.0	.	83	P14679	TYRO_HUMAN	I	83	ENSP00000263321:V83I	.	V	+	1	0	TYR	88551016	1.000000	0.71417	0.451000	0.26982	0.487000	0.33371	5.367000	0.66127	0.462000	0.27095	-0.940000	0.02684	GTC	G|1.000;A|0.000	0.000	weak		0.512	TYR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394045.2	NM_000372	
SYNDIG1L	646658	hgsc.bcm.edu	37	14	74876355	74876355	+	Missense_Mutation	SNP	G	G	C	rs61734850	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr14:74876355G>C	ENST00000554823.1	-	1	154	c.93C>G	c.(91-93)agC>agG	p.S31R	SYNDIG1L_ENST00000331628.3_Missense_Mutation_p.S31R			A6NDD5	SYN1L_HUMAN	synapse differentiation inducing 1-like	31					response to biotic stimulus (GO:0009607)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|endometrium(1)|lung(8)|pancreas(1)|prostate(1)|skin(1)	14						GGCAGGACCAGCTGGGTGGGG	0.657													G|||	521	0.104034	0.0983	0.1945	5008	,	,		16521	0.0813		0.1203	False		,,,				2504	0.0542				p.S31R		Atlas-SNP	.											.	SYNDIG1L	24	.	0			c.C93G						PASS	.	G	ARG/SER	397,3481		23,351,1565	35.0	41.0	39.0		93	3.5	1.0	14	dbSNP_129	39	919,7355		42,835,3260	yes	missense	SYNDIG1L	NM_001105579.1	110	65,1186,4825	CC,CG,GG		11.1071,10.2372,10.8295	benign	31/239	74876355	1316,10836	1939	4137	6076	SO:0001583	missense	646658	exon2			GGACCAGCTGGGT		CCDS41970.1	14q24.3	2011-06-30	2011-06-30	2011-06-30		ENSG00000183379			32388	protein-coding gene	gene with protein product	"""caudate-and putamen-enriched sequence"", ""interferon induced transmembrane protein domain containing 4"""	609999	"""transmembrane protein 90A"""	TMEM90A		16359841	Standard	NM_001105579		Approved	capucin, IFITMD4	uc001xpx.2	A6NDD5		ENST00000554823.1:c.93C>G	14.37:g.74876355G>C	ENSP00000450439:p.Ser31Arg	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	98	4	0.0408163	NM_001105579		Missense_Mutation	SNP	ENST00000554823.1	37	CCDS41970.1	276	0.12637362637362637	57	0.11585365853658537	61	0.1685082872928177	59	0.10314685314685315	99	0.13060686015831136	G	9.554	1.116787	0.20795	0.102372	0.111071	ENSG00000183379	ENST00000331628;ENST00000554823;ENST00000554953	D;D	0.95377	-3.69;-3.69	4.44	3.46	0.39613	.	0.354560	0.30742	N	0.008976	T	0.02119	0.0066	N	0.19112	0.55	0.34750	P	0.268374	B	0.29085	0.232	B	0.32533	0.147	T	0.60439	-0.7263	9	0.72032	D	0.01	0.8397	9.8782	0.41216	0.165:0.0:0.835:0.0	rs61734850	31	A6NDD5	SYN1L_HUMAN	R	31	ENSP00000331474:S31R;ENSP00000450439:S31R	ENSP00000331474:S31R	S	-	3	2	SYNDIG1L	73946108	0.978000	0.34361	1.000000	0.80357	0.240000	0.25518	1.104000	0.31074	2.298000	0.77334	0.467000	0.42956	AGC	G|0.868;C|0.132	0.132	strong		0.657	SYNDIG1L-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412341.1	XM_938515	
MARVELD3	91862	hgsc.bcm.edu	37	16	71660310	71660310	+	Missense_Mutation	SNP	G	G	A	rs4788821	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr16:71660310G>A	ENST00000268485.3	+	1	222	c.178G>A	c.(178-180)Gag>Aag	p.E60K	MARVELD3_ENST00000567566.1_Missense_Mutation_p.E60K|RP11-432I5.2_ENST00000562763.1_RNA|MARVELD3_ENST00000565261.1_Missense_Mutation_p.E60K|MARVELD3_ENST00000567501.1_5'Flank|MARVELD3_ENST00000299952.4_Missense_Mutation_p.E60K	NM_052858.4	NP_443090.4	Q96A59	MALD3_HUMAN	MARVEL domain containing 3	60	Arg-rich.		E -> K (in dbSNP:rs4788821). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		cell-cell junction organization (GO:0045216)|tight junction assembly (GO:0070830)	cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|tight junction (GO:0005923)				NS(1)|endometrium(3)|large_intestine(5)|lung(6)|skin(2)	17		Ovarian(137;0.125)				CCGGGACCCGGAGAGAGACCA	0.731													G|||	2072	0.413738	0.2451	0.5231	5008	,	,		11452	0.7421		0.325	False		,,,				2504	0.317				p.E60K		Atlas-SNP	.											.	MARVELD3	63	.	0			c.G178A						PASS	.	G	LYS/GLU,LYS/GLU	875,2933		104,667,1133	33.0	51.0	45.0		178,178	1.2	0.0	16	dbSNP_111	45	2199,5223		322,1555,1834	yes	missense,missense	MARVELD3	NM_052858.3,NM_001017967.2	56,56	426,2222,2967	AA,AG,GG		29.6281,22.9779,27.3731	benign,benign	60/402,60/411	71660310	3074,8156	1904	3711	5615	SO:0001583	missense	91862	exon1			GACCCGGAGAGAG	BC013376	CCDS10904.1, CCDS32478.1, CCDS59270.1	16q22.2	2008-02-05	2004-07-12	2004-07-14	ENSG00000140832	ENSG00000140832			30525	protein-coding gene	gene with protein product		614094	"""MARVEL (membrane-associating) domain containing 3"""	MRVLDC3			Standard	NM_001017967		Approved		uc002fat.4	Q96A59	OTTHUMG00000137591	ENST00000268485.3:c.178G>A	16.37:g.71660310G>A	ENSP00000268485:p.Glu60Lys	Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	200	11	0.055	NM_001017967	A8K820|H3BQM5|Q96MJ4	Missense_Mutation	SNP	ENST00000268485.3	37	CCDS10904.1	936	0.42857142857142855	120	0.24390243902439024	164	0.4530386740331492	414	0.7237762237762237	238	0.31398416886543534	G	12.99	2.104181	0.37145	0.229779	0.296281	ENSG00000140832	ENST00000268485;ENST00000299952	T;T	0.56444	0.46;0.46	2.15	1.17	0.20885	.	3.055740	0.01243	U	0.008678	T	0.00012	0.0000	L	0.34521	1.04	0.09310	P	0.9999999999985243	B;B	0.30889	0.159;0.299	B;B	0.17098	0.017;0.017	T	0.43605	-0.9381	9	0.18276	T	0.48	.	6.0428	0.19744	0.1747:0.0:0.8253:0.0	rs4788821;rs17262334;rs17845037;rs17856380;rs17856423;rs17857810;rs52819161;rs59320056;rs4788821	60;60	Q96A59-2;Q96A59	.;MALD3_HUMAN	K	60	ENSP00000268485:E60K;ENSP00000299952:E60K	ENSP00000268485:E60K	E	+	1	0	MARVELD3	70217811	0.017000	0.18338	0.002000	0.10522	0.013000	0.08279	1.980000	0.40618	0.129000	0.18514	0.298000	0.19748	GAG	G|0.561;A|0.439	0.439	strong		0.731	MARVELD3-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000268991.2	NM_052858	
DDX47	51202	hgsc.bcm.edu	37	12	12967127	12967127	+	Silent	SNP	C	C	T	rs1051374	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr12:12967127C>T	ENST00000358007.3	+	2	172	c.150C>T	c.(148-150)atC>atT	p.I50I	DDX47_ENST00000352940.4_Silent_p.I50I	NM_016355.3	NP_057439.2	Q9H0S4	DDX47_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 47	50					extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|mRNA processing (GO:0006397)|RNA splicing (GO:0008380)|rRNA processing (GO:0006364)	membrane (GO:0016020)|nucleolus (GO:0005730)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	16		Prostate(47;0.0526)		BRCA - Breast invasive adenocarcinoma(232;0.0354)		CCACCAAGATCCAGATTGAAG	0.398													C|||	1937	0.386781	0.2511	0.4121	5008	,	,		23125	0.5992		0.2734	False		,,,				2504	0.4499				p.I50I		Atlas-SNP	.											.	DDX47	37	.	0			c.C150T						PASS	.	C	,	1166,3240	412.4+/-336.1	168,830,1205	308.0	290.0	296.0		150,150	5.3	1.0	12	dbSNP_86	296	2385,6215	397.3+/-345.7	330,1725,2245	yes	coding-synonymous,coding-synonymous	DDX47	NM_016355.3,NM_201224.1	,	498,2555,3450	TT,TC,CC		27.7326,26.4639,27.3028	,	50/456,50/407	12967127	3551,9455	2203	4300	6503	SO:0001819	synonymous_variant	51202	exon2			CAAGATCCAGATT	AK127712	CCDS8655.1, CCDS8656.1	12p13.2	2010-07-06			ENSG00000213782	ENSG00000213782		"""DEAD-boxes"""	18682	protein-coding gene	gene with protein product		615428					Standard	NM_016355		Approved	DKFZp564O176, FLJ30012, HQ0256, RRP3	uc001rax.3	Q9H0S4	OTTHUMG00000168709	ENST00000358007.3:c.150C>T	12.37:g.12967127C>T		Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	207	13	0.0628019	NM_201224	B3KXP4|G5E955|Q96GM0|Q96NV8|Q9UI98	Silent	SNP	ENST00000358007.3	37	CCDS8655.1																																																																																			C|0.686;T|0.314	0.314	strong		0.398	DDX47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400674.1	NM_016355	
FOXD4L1	200350	hgsc.bcm.edu	37	2	114257354	114257354	+	Missense_Mutation	SNP	A	A	G	rs202243377	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr2:114257354A>G	ENST00000306507.5	+	1	694	c.521A>G	c.(520-522)cAc>cGc	p.H174R		NM_012184.4	NP_036316.1	Q9NU39	FX4L1_HUMAN	forkhead box D4-like 1	174					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(10)|prostate(1)|skin(2)	26						GAGCCGGGCCACCCAGGCAAG	0.632													.|||	294	0.0587061	0.0091	0.0908	5008	,	,		10222	0.1776		0.0139	False		,,,				2504	0.0266				p.H174R		Atlas-SNP	.											FOXD4L1,NS,carcinoma,0,1	FOXD4L1	48	1	0			c.A521G						scavenged	.						75.0	97.0	89.0					2																	114257354		2141	4139	6280	SO:0001583	missense	200350	exon1			CGGGCCACCCAGG	AF452723	CCDS2117.1	2q14.1	2008-02-05			ENSG00000184492	ENSG00000184492			18521	protein-coding gene	gene with protein product		611084				12421752, 15233989	Standard	NM_012184		Approved	FOXD5	uc002tjw.4	Q9NU39	OTTHUMG00000131359	ENST00000306507.5:c.521A>G	2.37:g.114257354A>G	ENSP00000302756:p.His174Arg	Somatic	65	4	0.0615385		WXS	Illumina HiSeq	Phase_I	76	12	0.157895	NM_012184	B3KWN1|B9EGF3	Missense_Mutation	SNP	ENST00000306507.5	37	CCDS2117.1	.	.	.	.	.	.	.	.	.	.	.	11.09	1.536728	0.27475	.	.	ENSG00000184492	ENST00000306507	D	0.95069	-3.6	2.57	2.57	0.30868	Winged helix-turn-helix transcription repressor DNA-binding (1);Transcription factor, fork head (3);	0.000000	0.35739	U	0.003002	T	0.78426	0.4281	N	0.00471	-1.455	0.41757	D	0.989692	B	0.14012	0.009	B	0.15052	0.012	T	0.71768	-0.4493	10	0.24483	T	0.36	.	8.6531	0.34046	1.0:0.0:0.0:0.0	.	174	Q9NU39	FX4L1_HUMAN	R	174	ENSP00000302756:H174R	ENSP00000302756:H174R	H	+	2	0	FOXD4L1	113973824	0.878000	0.30173	1.000000	0.80357	0.878000	0.50629	5.717000	0.68446	1.190000	0.43042	0.155000	0.16302	CAC	A|0.999;G|0.001	0.001	weak		0.632	FOXD4L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254148.1	NM_012184	
ZC2HC1C	79696	hgsc.bcm.edu	37	14	75537381	75537381	+	Silent	SNP	C	C	T	rs11546525	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr14:75537381C>T	ENST00000524913.1	+	2	594	c.105C>T	c.(103-105)taC>taT	p.Y35Y	ACYP1_ENST00000555463.1_5'Flank|ZC2HC1C_ENST00000439583.2_Silent_p.Y35Y|ZC2HC1C_ENST00000238686.8_Silent_p.Y35Y|ZC2HC1C_ENST00000526748.1_Intron	NM_024643.2	NP_078919.2	Q53FD0	ZC21C_HUMAN	zinc finger, C2HC-type containing 1C	35							metal ion binding (GO:0046872)										AAGACTCTTACGAACAAGGTG	0.517													C|||	1749	0.349241	0.0257	0.4236	5008	,	,		18283	0.6468		0.4513	False		,,,				2504	0.3221				p.Y35Y		Atlas-SNP	.											FAM164C,colon,carcinoma,0,3	.	.	3	0			c.C105T						PASS	.	C	,	372,3508		18,336,1586	91.0	90.0	90.0		105,105	1.1	0.9	14	dbSNP_120	90	3455,4855		712,2031,1412	no	coding-synonymous,coding-synonymous	FAM164C	NM_001042430.1,NM_024643.2	,	730,2367,2998	TT,TC,CC		41.5764,9.5876,31.3946	,	35/276,35/457	75537381	3827,8363	1940	4155	6095	SO:0001819	synonymous_variant	79696	exon2			CTCTTACGAACAA	AK026746	CCDS41972.1, CCDS45138.1	14q24.3	2013-01-10	2012-02-03	2012-02-03	ENSG00000119703	ENSG00000119703		"""Zinc fingers, C2HC-type containing"""	20354	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 140"", ""family with sequence similarity 164, member C"""	C14orf140, FAM164C			Standard	XM_005268062		Approved		uc001xrh.3	Q53FD0	OTTHUMG00000167439	ENST00000524913.1:c.105C>T	14.37:g.75537381C>T		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	108	8	0.0740741	NM_024643	E9PJQ0|Q9BTA8|Q9H5S9	Silent	SNP	ENST00000524913.1	37	CCDS41972.1																																																																																			C|0.608;T|0.392	0.392	strong		0.517	ZC2HC1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394616.4	NM_001042430	
ZNF879	345462	hgsc.bcm.edu	37	5	178459426	178459426	+	Missense_Mutation	SNP	A	A	C	rs17078991	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr5:178459426A>C	ENST00000444149.2	+	5	665	c.477A>C	c.(475-477)gaA>gaC	p.E159D		NM_001136116.1	NP_001129588.1	B4DU55	ZN879_HUMAN	zinc finger protein 879	159					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)	p.E159D(1)		endometrium(3)|kidney(2)|pancreas(1)|stomach(1)	7						AAGGTGTTGAATTTGGGAAAA	0.373													A|||	1824	0.364217	0.5182	0.255	5008	,	,		19198	0.4276		0.2237	False		,,,				2504	0.3129				p.E159D		Atlas-SNP	.											ZNF879,NS,carcinoma,0,2	ZNF879	41	2	1	Substitution - Missense(1)	stomach(1)	c.A477C						scavenged	.	A	ASP/GLU	618,766		138,342,212	91.0	77.0	81.0		477	-1.2	0.3	5	dbSNP_123	81	706,2476		75,556,960	yes	missense	ZNF879	NM_001136116.1	45	213,898,1172	CC,CA,AA		22.1873,44.6532,28.9969	benign	159/564	178459426	1324,3242	692	1591	2283	SO:0001583	missense	345462	exon5			TGTTGAATTTGGG	AK300504	CCDS47352.1	5q35.3	2013-01-08			ENSG00000234284	ENSG00000234284		"""Zinc fingers, C2H2-type"", ""-"""	37273	protein-coding gene	gene with protein product							Standard	NM_001136116		Approved	DKFZp686E2433	uc003mjt.4	B4DU55	OTTHUMG00000163596	ENST00000444149.2:c.477A>C	5.37:g.178459426A>C	ENSP00000414887:p.Glu159Asp	Somatic	321	2	0.00623053		WXS	Illumina HiSeq	Phase_I	282	11	0.0390071	NM_001136116		Missense_Mutation	SNP	ENST00000444149.2	37	CCDS47352.1	770	0.3525641025641026	243	0.49390243902439024	100	0.27624309392265195	244	0.42657342657342656	183	0.24142480211081793	A	9.372	1.070780	0.20147	0.446532	0.221873	ENSG00000234284	ENST00000444149	T	0.06933	3.24	4.45	-1.18	0.09617	.	.	.	.	.	T	0.00012	0.0000	L	0.37850	1.14	0.34582	P	0.28547900000000004	B	0.02656	0.0	B	0.04013	0.001	T	0.42120	-0.9470	8	0.42905	T	0.14	-4.0842	4.6168	0.12430	0.4554:0.3309:0.2137:0.0	rs17078991;rs52798739;rs17078991	159	B4DU55	ZN879_HUMAN	D	159	ENSP00000414887:E159D	ENSP00000414887:E159D	E	+	3	2	ZNF879	178392032	0.000000	0.05858	0.286000	0.24833	0.782000	0.44232	-0.068000	0.11561	-0.283000	0.09115	0.482000	0.46254	GAA	A|0.634;C|0.366	0.366	strong		0.373	ZNF879-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374447.1	NM_001136116	
CCDC176	80127	hgsc.bcm.edu	37	14	74514674	74514674	+	Missense_Mutation	SNP	A	A	T	rs3784038	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr14:74514674A>T	ENST00000394009.3	+	7	812	c.689A>T	c.(688-690)gAt>gTt	p.D230V	CCDC176_ENST00000489323.1_3'UTR|AC005484.5_ENST00000492026.1_RNA|CCDC176_ENST00000553773.1_5'UTR	NM_025057.2	NP_079333.2	Q8ND07	BBOF1_HUMAN	coiled-coil domain containing 176	230			D -> V (in dbSNP:rs3784038). {ECO:0000269|PubMed:17974005}.		motile cilium assembly (GO:0044458)	ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)											AAAGAGAATGATTATCTTCAG	0.348													T|||	3164	0.631789	0.5454	0.5274	5008	,	,		17876	0.8829		0.4751	False		,,,				2504	0.7249				p.D230V		Atlas-SNP	.											.	.	.	.	0			c.A689T						PASS	.	T	VAL/ASP	1750,1386		483,784,301	80.0	71.0	74.0		689	5.8	1.0	14	dbSNP_107	74	3432,3732		818,1796,968	yes	missense	C14orf45	NM_025057.2	152	1301,2580,1269	TT,TA,AA		47.9062,44.1964,49.6893	benign	230/530	74514674	5182,5118	1568	3582	5150	SO:0001583	missense	80127	exon7			AGAATGATTATCT	BI457605	CCDS32119.2	14q24.3	2013-01-04	2012-09-25	2012-09-25	ENSG00000119636	ENSG00000119636			19855	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 45"""	C14orf45			Standard	NM_025057		Approved		uc010tup.2	Q8ND07	OTTHUMG00000152786	ENST00000394009.3:c.689A>T	14.37:g.74514674A>T	ENSP00000377577:p.Asp230Val	Somatic	258	0	0		WXS	Illumina HiSeq	Phase_I	236	14	0.059322	NM_025057	Q0P604|Q9H5P8	Missense_Mutation	SNP	ENST00000394009.3	37	CCDS32119.2	1311	0.6002747252747253	262	0.532520325203252	181	0.5	503	0.8793706293706294	365	0.4815303430079156	T	15.43	2.830233	0.50845	0.558036	0.479062	ENSG00000119636	ENST00000464394;ENST00000394009	T;T	0.32023	1.47;1.47	5.78	5.78	0.91487	.	0.403487	0.24776	N	0.035682	T	0.00012	0.0000	N	0.00069	-2.28	0.09310	P	0.9999999999999967	B	0.02656	0.0	B	0.01281	0.0	T	0.35968	-0.9767	9	0.26408	T	0.33	-1.8317	12.1639	0.54119	0.1283:0.0:0.0:0.8717	rs3784038;rs52825587;rs57060702;rs3784038	230	Q8ND07	CN045_HUMAN	V	90;230	ENSP00000451659:D90V;ENSP00000377577:D230V	ENSP00000377577:D230V	D	+	2	0	C14orf45	73584427	1.000000	0.71417	0.998000	0.56505	0.832000	0.47134	2.691000	0.47010	1.018000	0.39521	-0.265000	0.10407	GAT	A|0.410;T|0.590	0.590	strong		0.348	CCDC176-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327863.1	NM_025057	
PYGB	5834	hgsc.bcm.edu	37	20	25264786	25264786	+	Missense_Mutation	SNP	T	T	C			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr20:25264786T>C	ENST00000216962.4	+	14	1777	c.1667T>C	c.(1666-1668)gTg>gCg	p.V556A		NM_002862.3	NP_002853.2	P11216	PYGB_HUMAN	phosphorylase, glycogen; brain	556					carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	glycogen phosphorylase activity (GO:0008184)|pyridoxal phosphate binding (GO:0030170)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(12)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	31						GAGTACAAGGTGAAGATCAAC	0.537																																					p.V556A		Atlas-SNP	.											.	PYGB	84	.	0			c.T1667C						PASS	.						216.0	150.0	173.0					20																	25264786		2203	4300	6503	SO:0001583	missense	5834	exon14			ACAAGGTGAAGAT		CCDS13171.1	20p11.21	2013-03-01			ENSG00000100994	ENSG00000100994	2.4.1.1	"""Glycogen phosphorylases"""	9723	protein-coding gene	gene with protein product	"""glycogen phosphorylase, brain form"""	138550					Standard	NM_002862		Approved		uc002wup.3	P11216	OTTHUMG00000032117	ENST00000216962.4:c.1667T>C	20.37:g.25264786T>C	ENSP00000216962:p.Val556Ala	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	87	25	0.287356	NM_002862	Q96AK1|Q9NPX8	Missense_Mutation	SNP	ENST00000216962.4	37	CCDS13171.1	.	.	.	.	.	.	.	.	.	.	T	17.89	3.498726	0.64298	.	.	ENSG00000100994	ENST00000216962	D	0.95069	-3.6	3.86	3.86	0.44501	.	0.060202	0.64402	D	0.000005	D	0.95802	0.8634	M	0.90870	3.155	0.80722	D	1	B	0.28208	0.203	B	0.37601	0.254	D	0.96223	0.9162	10	0.87932	D	0	-22.5788	12.7816	0.57480	0.0:0.0:0.0:1.0	.	556	P11216	PYGB_HUMAN	A	556	ENSP00000216962:V556A	ENSP00000216962:V556A	V	+	2	0	PYGB	25212786	1.000000	0.71417	1.000000	0.80357	0.892000	0.51952	7.626000	0.83164	1.761000	0.52028	0.379000	0.24179	GTG	.	.	none		0.537	PYGB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078415.2	NM_002862	
MYO18A	399687	hgsc.bcm.edu	37	17	27448927	27448927	+	Missense_Mutation	SNP	C	C	T	rs201811476	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr17:27448927C>T	ENST00000527372.1	-	4	1316	c.1136G>A	c.(1135-1137)cGt>cAt	p.R379H	MYO18A_ENST00000354329.4_Missense_Mutation_p.R379H|MYO18A_ENST00000531253.1_Missense_Mutation_p.R379H|MYO18A_ENST00000533112.1_Missense_Mutation_p.R379H	NM_078471.3	NP_510880.2	Q92614	MY18A_HUMAN	myosin XVIIIA	379	Mediates nucleotide-independent binding to F-actin and interaction with GOLPH3.				actomyosin structure organization (GO:0031032)|cell migration (GO:0016477)|DNA metabolic process (GO:0006259)|Golgi organization (GO:0007030)|Golgi vesicle budding (GO:0048194)|negative regulation of apoptotic process (GO:0043066)|positive regulation of protein secretion (GO:0050714)	actomyosin (GO:0042641)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|myosin complex (GO:0016459)|trans-Golgi network (GO:0005802)	actin filament binding (GO:0051015)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|motor activity (GO:0003774)|poly(A) RNA binding (GO:0044822)			NS(1)|cervix(1)|endometrium(6)|kidney(6)|lung(20)|urinary_tract(2)	36			Epithelial(11;4.97e-05)|BRCA - Breast invasive adenocarcinoma(11;0.000221)|all cancers(11;0.000234)|Colorectal(6;0.0102)|COAD - Colon adenocarcinoma(6;0.031)			CAGCTTCACACGCACCTTCCC	0.612													C|||	2	0.000399361	0.0	0.0014	5008	,	,		18179	0.0		0.001	False		,,,				2504	0.0				p.R379H	Esophageal Squamous(182;472 2015 7001 15270 22562)	Atlas-SNP	.											.	MYO18A	217	.	0			c.G1136A						PASS	.	C	HIS/ARG,HIS/ARG	1,4183		0,1,2091	112.0	113.0	113.0		1136,1136	5.6	1.0	17		113	0,8444		0,0,4222	no	missense,missense	MYO18A	NM_078471.3,NM_203318.1	29,29	0,1,6313	TT,TC,CC		0.0,0.0239,0.0079	probably-damaging,probably-damaging	379/2055,379/2040	27448927	1,12627	2092	4222	6314	SO:0001583	missense	399687	exon4			TTCACACGCACCT	D86970	CCDS45641.1, CCDS45642.1	17q11.2	2011-09-27			ENSG00000196535	ENSG00000196535		"""Myosins / Myosin superfamily : Class XVIII"""	31104	protein-coding gene	gene with protein product		610067				12761286	Standard	NM_078471		Approved	KIAA0216, MysPDZ	uc002hdt.1	Q92614	OTTHUMG00000166360	ENST00000527372.1:c.1136G>A	17.37:g.27448927C>T	ENSP00000437073:p.Arg379His	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	49	17	0.346939	NM_078471	Q5H9U3|Q5W9F9|Q5W9G1|Q8IXP8	Missense_Mutation	SNP	ENST00000527372.1	37	CCDS45642.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	C	21.6	4.171334	0.78452	2.39E-4	0.0	ENSG00000196535	ENST00000354329;ENST00000359450;ENST00000533112;ENST00000531253;ENST00000527372;ENST00000531686	T;T;T;T	0.72282	-0.64;-0.64;-0.64;-0.64	5.64	5.64	0.86602	.	0.054581	0.64402	D	0.000001	T	0.69160	0.3080	L	0.46157	1.445	0.37405	D	0.91299	P;D;D;D	0.63046	0.873;0.983;0.983;0.992	B;P;P;P	0.51582	0.26;0.674;0.584;0.477	T	0.74393	-0.3680	10	0.54805	T	0.06	.	7.7622	0.28959	0.0:0.8021:0.0:0.1979	.	48;379;379;379	Q92614-2;Q92614-3;Q92614-4;Q92614	.;.;.;MY18A_HUMAN	H	379;379;379;379;379;59	ENSP00000346291:R379H;ENSP00000435932:R379H;ENSP00000434228:R379H;ENSP00000437073:R379H	ENSP00000346291:R379H	R	-	2	0	MYO18A	24473053	0.999000	0.42202	0.963000	0.40424	0.991000	0.79684	3.661000	0.54503	2.655000	0.90218	0.655000	0.94253	CGT	C|0.999;T|0.001	0.001	strong		0.612	MYO18A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389396.1	NM_078471	
HRH3	11255	hgsc.bcm.edu	37	20	60791422	60791422	+	Silent	SNP	C	C	T	rs3787430	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr20:60791422C>T	ENST00000340177.5	-	3	1262	c.978G>A	c.(976-978)ccG>ccA	p.P326P	HRH3_ENST00000317393.6_Silent_p.P326P	NM_007232.2	NP_009163.2	Q9Y5N1	HRH3_HUMAN	histamine receptor H3	326					brain development (GO:0007420)|drinking behavior (GO:0042756)|eating behavior (GO:0042755)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|learning (GO:0007612)|memory (GO:0007613)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of blood pressure (GO:0045776)|negative regulation of gamma-aminobutyric acid secretion (GO:0014053)|negative regulation of glutamate secretion (GO:0014050)|negative regulation of serotonin secretion (GO:0014063)|neurotransmitter secretion (GO:0007269)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of epithelial cell proliferation (GO:0050679)|regulation of norepinephrine secretion (GO:0014061)|response to organic cyclic compound (GO:0014070)	integral component of plasma membrane (GO:0005887)|myelin sheath (GO:0043209)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	drug binding (GO:0008144)|histamine receptor activity (GO:0004969)			breast(1)|endometrium(1)|lung(4)|skin(2)|upper_aerodigestive_tract(1)	9	Breast(26;7.76e-09)		BRCA - Breast invasive adenocarcinoma(19;7.08e-07)		Betahistine(DB06698)|Histamine Phosphate(DB00667)|Mirtazapine(DB00370)	AGGACGCCGACGGCTTGGAGC	0.677													C|||	891	0.177915	0.1846	0.1513	5008	,	,		14281	0.1815		0.1441	False		,,,				2504	0.2188				p.P326P		Atlas-SNP	.											.	HRH3	25	.	0			c.G978A						PASS	.	C		787,3601		82,623,1489	11.0	11.0	11.0		978	-9.1	0.2	20	dbSNP_107	11	1221,7339		105,1011,3164	no	coding-synonymous	HRH3	NM_007232.2		187,1634,4653	TT,TC,CC		14.264,17.9353,15.5082		326/446	60791422	2008,10940	2194	4280	6474	SO:0001819	synonymous_variant	11255	exon3			CGCCGACGGCTTG	AF140538	CCDS13493.1	20q13.33	2013-09-19			ENSG00000101180	ENSG00000101180		"""GPCR / Class A : Histamine receptors"""	5184	protein-coding gene	gene with protein product		604525				10347254	Standard	NM_007232		Approved	GPCR97	uc002ycf.2	Q9Y5N1	OTTHUMG00000032899	ENST00000340177.5:c.978G>A	20.37:g.60791422C>T		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	69	5	0.0724638	NM_007232	Q4QRI7|Q9GZX2|Q9H4K8	Silent	SNP	ENST00000340177.5	37	CCDS13493.1																																																																																			C|0.833;T|0.167	0.167	strong		0.677	HRH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079994.1	NM_007232	
TAS2R43	259289	hgsc.bcm.edu	37	12	11244725	11244725	+	Missense_Mutation	SNP	C	C	G	rs68157013	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr12:11244725C>G	ENST00000531678.1	-	1	187	c.104G>C	c.(103-105)tGg>tCg	p.W35S	PRR4_ENST00000536668.1_Intron|TAS2R14_ENST00000381852.4_Intron	NM_176884.2	NP_795365.2	P59537	T2R43_HUMAN	taste receptor, type 2, member 43	35				W -> S (in Ref. 1; AAM19328, 3; AAU21145 and 5; AAI17424). {ECO:0000305}.	detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|G-protein coupled receptor signaling pathway (GO:0007186)	integral component of membrane (GO:0016021)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)|taste receptor activity (GO:0008527)			endometrium(1)|ovary(1)|prostate(2)|urinary_tract(1)	5			OV - Ovarian serous cystadenocarcinoma(49;0.0344)	BRCA - Breast invasive adenocarcinoma(232;0.196)		TCTCTTGAACCACTCAATGGA	0.383													.|||	3113	0.621605	0.0976	0.7118	5008	,	,		11851	0.9425		0.7525	False		,,,				2504	0.8006				p.W35S		Atlas-SNP	.											TAS2R46_ENST00000422992,NS,carcinoma,0,4	TAS2R43	19	4	0			c.G104C						PASS	.						45.0	39.0	41.0					12																	11244725		1858	3572	5430	SO:0001583	missense	259289	exon1			TTGAACCACTCAA	AF494237	CCDS53749.1	12p13.2	2012-08-22				ENSG00000255374		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	18875	protein-coding gene	gene with protein product		612668				12379855	Standard	NM_176884		Approved	T2R52	uc001qzq.1	P59537		ENST00000531678.1:c.104G>C	12.37:g.11244725C>G	ENSP00000431719:p.Trp35Ser	Somatic	10	0	0		WXS	Illumina HiSeq	Phase_I	27	18	0.666667	NM_176884	P59546|Q645X4	Missense_Mutation	SNP	ENST00000531678.1	37	CCDS53749.1	926	0.423992673992674	31	0.06300813008130081	161	0.4447513812154696	418	0.7307692307692307	316	0.41688654353562005	-	1.291	-0.607724	0.03717	.	.	ENSG00000255374	ENST00000531678	T	0.01113	5.32	1.97	0.939	0.19506	.	.	.	.	.	T	0.00012	0.0000	H	0.97051	3.93	0.30802	P	0.739796	.	.	.	.	.	.	T	0.26573	-1.0099	6	0.72032	D	0.01	.	5.2922	0.15733	0.3385:0.6615:0.0:0.0	.	.	.	.	S	35	ENSP00000431719:W35S	ENSP00000431719:W35S	W	-	2	0	TAS2R43	11135992	0.155000	0.22806	0.246000	0.24233	0.092000	0.18411	1.065000	0.30592	0.107000	0.17824	0.184000	0.17185	TGG	C|0.597;G|0.403	0.403	strong		0.383	TAS2R43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383561.1	NM_176884	
IKBKB	3551	hgsc.bcm.edu	37	8	42176069	42176069	+	Splice_Site	SNP	G	G	T			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr8:42176069G>T	ENST00000520810.1	+	13	1426		c.e13-1		IKBKB_ENST00000379708.3_Splice_Site|IKBKB_ENST00000416505.2_Splice_Site|IKBKB_ENST00000522147.1_Intron|IKBKB_ENST00000520835.1_Splice_Site	NM_001556.2	NP_001547.1	O14920	IKKB_HUMAN	inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase beta						B cell homeostasis (GO:0001782)|cellular response to tumor necrosis factor (GO:0071356)|Fc-epsilon receptor signaling pathway (GO:0038095)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|I-kappaB phosphorylation (GO:0007252)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of cation channel activity (GO:2001259)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sodium ion transport (GO:0010765)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein phosphorylation (GO:0006468)|response to virus (GO:0009615)|serine phosphorylation of STAT protein (GO:0042501)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	CD40 receptor complex (GO:0035631)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|IkappaB kinase complex (GO:0008385)|nucleus (GO:0005634)	ATP binding (GO:0005524)|IkappaB kinase activity (GO:0008384)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|scaffold protein binding (GO:0097110)			breast(4)|lung(1)|ovary(2)|skin(1)	8	all_cancers(6;1.42e-24)|all_epithelial(6;1.02e-25)|all_lung(13;6.21e-12)|Lung NSC(13;1.04e-10)|Ovarian(28;0.00769)|Prostate(17;0.0119)|Colorectal(14;0.0468)|Lung SC(25;0.211)	all_lung(54;0.000434)|Lung NSC(58;0.00161)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.0954)	BRCA - Breast invasive adenocarcinoma(8;1.37e-10)|Colorectal(10;0.00102)|OV - Ovarian serous cystadenocarcinoma(14;0.00168)|Lung(22;0.00467)|LUSC - Lung squamous cell carcinoma(45;0.024)|COAD - Colon adenocarcinoma(11;0.0264)		Acetylcysteine(DB06151)|Acetylsalicylic acid(DB00945)|Arsenic trioxide(DB01169)|Auranofin(DB00995)|Mesalazine(DB00244)|Sulfasalazine(DB00795)	TCTGTCTCCAGTTCAAGAGCC	0.493																																					.		Atlas-SNP	.											.	IKBKB	88	.	0			c.1064-1G>T						PASS	.						89.0	86.0	87.0					8																	42176069		2203	4300	6503	SO:0001630	splice_region_variant	3551	exon12			TCTCCAGTTCAAG	AF029684	CCDS6128.1, CCDS55228.1, CCDS56535.1	8p11.2	2008-08-18			ENSG00000104365	ENSG00000104365			5960	protein-coding gene	gene with protein product		603258				9878263, 9763654	Standard	NM_001556		Approved	IKK2, NFKBIKB, IKK-beta, IKKB	uc003xow.2	O14920	OTTHUMG00000164092	ENST00000520810.1:c.1241-1G>T	8.37:g.42176069G>T		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	132	39	0.295455	NM_001242778	B4DZ30|B4E0U4|O75327	Splice_Site	SNP	ENST00000520810.1	37	CCDS6128.1	.	.	.	.	.	.	.	.	.	.	G	21.3	4.124132	0.77436	.	.	ENSG00000104365	ENST00000520810;ENST00000416505;ENST00000520835;ENST00000379708	.	.	.	5.81	5.81	0.92471	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.6681	0.95900	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	IKBKB	42295226	1.000000	0.71417	0.997000	0.53966	0.841000	0.47740	7.789000	0.85783	2.740000	0.93945	0.555000	0.69702	.	.	.	none		0.493	IKBKB-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377214.1		Intron
SMARCA2	6595	hgsc.bcm.edu	37	9	2039776	2039776	+	Silent	SNP	A	A	G	rs376509101|rs13296987	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr9:2039776A>G	ENST00000382203.1	+	4	875	c.666A>G	c.(664-666)caA>caG	p.Q222Q	SMARCA2_ENST00000349721.2_Silent_p.Q222Q|SMARCA2_ENST00000491574.1_3'UTR|SMARCA2_ENST00000357248.2_Silent_p.Q222Q|SMARCA2_ENST00000382194.1_Silent_p.Q222Q|RP11-264I13.2_ENST00000426860.1_RNA			P51531	SMCA2_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2	222	Poly-Gln.				aortic smooth muscle cell differentiation (GO:0035887)|ATP catabolic process (GO:0006200)|chromatin remodeling (GO:0006338)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)	intermediate filament cytoskeleton (GO:0045111)|intracellular membrane-bounded organelle (GO:0043231)|nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	ATP binding (GO:0005524)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)|RNA polymerase II transcription coactivator activity (GO:0001105)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(11)|liver(2)|lung(19)|ovary(3)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	56		all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09)		GBM - Glioblastoma multiforme(50;0.0475)		agcagcagcaacagcagcagc	0.637													A|||	80	0.0159744	0.0333	0.0029	5008	,	,		13171	0.001		0.004	False		,,,				2504	0.0297				p.Q222Q		Atlas-SNP	.											SMARCA2_ENST00000349721,NS,carcinoma,0,2	SMARCA2	313	2	0			c.A666G						PASS	.						12.0	14.0	13.0					9																	2039776		2197	4275	6472	SO:0001819	synonymous_variant	6595	exon4			GCAGCAACAGCAG	D26155	CCDS34977.1, CCDS34978.1, CCDS75807.1, CCDS75808.1	9p24.3	2008-11-11	2006-11-09		ENSG00000080503	ENSG00000080503			11098	protein-coding gene	gene with protein product		600014		SNF2L2		8012116	Standard	NM_003070		Approved	BAF190, hSNF2a, hBRM, Sth1p, SNF2LA, BRM, SNF2, SWI2	uc003zhc.3	P51531	OTTHUMG00000019445	ENST00000382203.1:c.666A>G	9.37:g.2039776A>G		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	86	7	0.0813954	NM_139045	B1ALG3|B1ALG4|D3DRH4|D3DRH5	Silent	SNP	ENST00000382203.1	37	CCDS34977.1																																																																																			A|0.750;G|0.250	0.250	strong		0.637	SMARCA2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000051505.1	NM_003070	
NPLOC4	55666	hgsc.bcm.edu	37	17	79580457	79580457	+	Silent	SNP	C	C	A	rs17852306	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr17:79580457C>A	ENST00000331134.6	-	4	488	c.273G>T	c.(271-273)acG>acT	p.T91T	NPLOC4_ENST00000539314.1_5'UTR|NPLOC4_ENST00000574344.1_5'UTR|NPLOC4_ENST00000374747.5_Silent_p.T91T	NM_017921.2	NP_060391.2	Q8TAT6	NPL4_HUMAN	nuclear protein localization 4 homolog (S. cerevisiae)	91					ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|Golgi organization (GO:0007030)|membrane fusion (GO:0061025)	endoplasmic reticulum (GO:0005783)|nuclear outer membrane-endoplasmic reticulum membrane network (GO:0042175)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)	11	all_neural(118;0.0878)|Melanoma(429;0.242)|all_lung(278;0.246)		BRCA - Breast invasive adenocarcinoma(99;0.0282)|OV - Ovarian serous cystadenocarcinoma(97;0.0739)			GTGGAACTGACGTCTCCATTT	0.512													C|||	428	0.0854633	0.053	0.0303	5008	,	,		17895	0.2212		0.0437	False		,,,				2504	0.0716				p.T91T		Atlas-SNP	.											.	NPLOC4	27	.	0			c.G273T						PASS	.	C		142,3802		1,140,1831	86.0	82.0	83.0		273	-8.4	0.2	17	dbSNP_123	83	337,7965		7,323,3821	no	coding-synonymous	NPLOC4	NM_017921.2		8,463,5652	AA,AC,CC		4.0593,3.6004,3.9115		91/609	79580457	479,11767	1972	4151	6123	SO:0001819	synonymous_variant	55666	exon4			AACTGACGTCTCC	AB040932	CCDS45812.1	17q25.3	2012-09-20			ENSG00000182446	ENSG00000182446			18261	protein-coding gene	gene with protein product		606590				11574150, 10811609	Standard	NM_017921		Approved	NPL4, FLJ20657, KIAA1499	uc002kas.3	Q8TAT6	OTTHUMG00000177990	ENST00000331134.6:c.273G>T	17.37:g.79580457C>A		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	96	7	0.0729167	NM_017921	Q8N3J1|Q9H8V2|Q9H964|Q9NWR5|Q9P229	Silent	SNP	ENST00000331134.6	37	CCDS45812.1																																																																																			C|0.916;A|0.084	0.084	strong		0.512	NPLOC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440140.1		
ABCA1	19	hgsc.bcm.edu	37	9	107620867	107620867	+	Missense_Mutation	SNP	C	C	T	rs2230806	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr9:107620867C>T	ENST00000374736.3	-	7	1050	c.656G>A	c.(655-657)aGg>aAg	p.R219K	ABCA1_ENST00000423487.2_Missense_Mutation_p.R219K	NM_005502.3	NP_005493.2	O95477	ABCA1_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 1	219			R -> K (common polymorphism; associated with a decreased severity of CAD; dbSNP:rs2230806). {ECO:0000269|PubMed:10938021, ECO:0000269|PubMed:11238261, ECO:0000269|PubMed:11257261, ECO:0000269|PubMed:11476965, ECO:0000269|PubMed:12624133, ECO:0000269|PubMed:12966036, ECO:0000269|PubMed:15520867}.		apolipoprotein A-I-mediated signaling pathway (GO:0038027)|cellular lipid metabolic process (GO:0044255)|cellular response to cholesterol (GO:0071397)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to retinoic acid (GO:0071300)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|endosomal transport (GO:0016197)|G-protein coupled receptor signaling pathway (GO:0007186)|high-density lipoprotein particle assembly (GO:0034380)|interleukin-1 beta secretion (GO:0050702)|intracellular cholesterol transport (GO:0032367)|lipoprotein metabolic process (GO:0042157)|lysosome organization (GO:0007040)|negative regulation of cholesterol storage (GO:0010887)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|peptide secretion (GO:0002790)|phagocytosis, engulfment (GO:0006911)|phospholipid efflux (GO:0033700)|phospholipid homeostasis (GO:0055091)|phospholipid translocation (GO:0045332)|platelet dense granule organization (GO:0060155)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cholesterol efflux (GO:0010875)|protein lipidation (GO:0006497)|regulation of Cdc42 protein signal transduction (GO:0032489)|response to drug (GO:0042493)|response to laminar fluid shear stress (GO:0034616)|response to low-density lipoprotein particle (GO:0055098)|response to nutrient (GO:0007584)|reverse cholesterol transport (GO:0043691)|small molecule metabolic process (GO:0044281)	endocytic vesicle (GO:0030139)|external side of plasma membrane (GO:0009897)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)	anion transmembrane transporter activity (GO:0008509)|apolipoprotein A-I binding (GO:0034186)|apolipoprotein A-I receptor activity (GO:0034188)|apolipoprotein binding (GO:0034185)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase binding (GO:0051117)|cholesterol binding (GO:0015485)|cholesterol transporter activity (GO:0017127)|phospholipid binding (GO:0005543)|phospholipid transporter activity (GO:0005548)|receptor binding (GO:0005102)|small GTPase binding (GO:0031267)|syntaxin binding (GO:0019905)	p.R219K(1)		NS(1)|autonomic_ganglia(1)|breast(5)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(31)|liver(1)|lung(40)|ovary(5)|pancreas(2)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	115				OV - Ovarian serous cystadenocarcinoma(323;0.023)	Adenosine triphosphate(DB00171)|Glyburide(DB01016)|Probucol(DB01599)	CAGTTTCTCCCTTGGTAGGCC	0.468													C|||	2202	0.439696	0.7103	0.3487	5008	,	,		19674	0.4147		0.2425	False		,,,				2504	0.3671				p.R219K		Atlas-SNP	.											ABCA1,NS,carcinoma,0,1	ABCA1	244	1	1	Substitution - Missense(1)	stomach(1)	c.G656A	GRCh37	CM030397	ABCA1	M	rs2230806	scavenged	.	C	LYS/ARG	2672,1734	648.2+/-398.7	820,1032,351	154.0	151.0	152.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	656	0.1	0.2	9	dbSNP_98	152	2420,6180	400.1+/-346.7	322,1776,2202	yes	missense	ABCA1	NM_005502.3	26	1142,2808,2553	TT,TC,CC		28.1395,39.3554,39.1512	benign	219/2262	107620867	5092,7914	2203	4300	6503	SO:0001583	missense	19	exon7			TTCTCCCTTGGTA	AJ012376	CCDS6762.1	9q31	2014-03-14			ENSG00000165029	ENSG00000165029		"""ATP binding cassette transporters / subfamily A"""	29	protein-coding gene	gene with protein product	"""Tangier disease"""	600046		ABC1, HDLDT1		8088782, 10431236, 10431237, 10431238	Standard	NM_005502		Approved	TGD	uc004bcl.3	O95477	OTTHUMG00000020417	ENST00000374736.3:c.656G>A	9.37:g.107620867C>T	ENSP00000363868:p.Arg219Lys	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	110	5	0.0454545	NM_005502	Q5VX33|Q96S56|Q96T85|Q9NQV4|Q9UN06|Q9UN07|Q9UN08|Q9UN09	Missense_Mutation	SNP	ENST00000374736.3	37	CCDS6762.1	916	0.4194139194139194	356	0.7235772357723578	127	0.35082872928176795	250	0.4370629370629371	183	0.24142480211081793	C	7.792	0.711767	0.15306	0.606446	0.281395	ENSG00000165029	ENST00000374736;ENST00000423487	D;D	0.94931	-2.23;-3.56	6.17	0.0573	0.14322	.	0.632115	0.18950	N	0.126712	T	0.00012	0.0000	N	0.04880	-0.145	0.28835	P	0.896936	B	0.02656	0.0	B	0.01281	0.0	T	0.46119	-0.9214	9	0.16896	T	0.51	.	8.2419	0.31665	0.0:0.3764:0.0:0.6236	rs2230806;rs2234884;rs2853572;rs52801000;rs61696010;rs2230806	219	O95477	ABCA1_HUMAN	K	219	ENSP00000363868:R219K;ENSP00000416623:R219K	ENSP00000363868:R219K	R	-	2	0	ABCA1	106660688	0.825000	0.29262	0.227000	0.23927	0.534000	0.34807	0.318000	0.19504	0.083000	0.17047	0.655000	0.94253	AGG	C|0.587;T|0.413	0.413	strong		0.468	ABCA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053491.1	NM_005502	
OR4M2	390538	hgsc.bcm.edu	37	15	22369426	22369426	+	Missense_Mutation	SNP	G	G	A	rs4087943	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr15:22369426G>A	ENST00000332663.2	+	1	949	c.851G>A	c.(850-852)cGt>cAt	p.R284H	RP11-69H14.6_ENST00000558896.1_RNA	NM_001004719.2	NP_001004719.2	Q8NGB6	OR4M2_HUMAN	olfactory receptor, family 4, subfamily M, member 2	284			R -> H (in dbSNP:rs4087943).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(2)|endometrium(2)|kidney(4)|large_intestine(6)|lung(38)|ovary(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)	63		all_cancers(20;1.94e-20)|all_epithelial(15;3.94e-18)|Lung NSC(15;8.53e-15)|all_lung(15;2.87e-14)|Breast(32;0.00519)|Colorectal(260;0.101)	GBM - Glioblastoma multiforme(6;0.124)	all cancers(64;1.64e-11)|Epithelial(43;5.81e-10)|BRCA - Breast invasive adenocarcinoma(123;0.000255)|Kidney(6;0.00736)|KIRC - Kidney renal clear cell carcinoma(6;0.0135)|GBM - Glioblastoma multiforme(186;0.0963)		TTCCCTTTACGTAATCCCATT	0.363																																					p.R284H		Atlas-SNP	.											OR4M2,colon,carcinoma,0,1	OR4M2	140	1	0			c.G851A						scavenged	.		HIS/ARG	1899,2507		127,1645,431	159.0	123.0	135.0		851	2.3	1.0	15	dbSNP_108	135	4802,3798		852,3098,350	no	missense	OR4M2	NM_001004719.2	29	979,4743,781	AA,AG,GG		44.1628,43.1003,48.4776	benign	284/314	22369426	6701,6305	2203	4300	6503	SO:0001583	missense	390538	exon1			CTTTACGTAATCC	AC060768	CCDS32172.1	15q11.2	2013-09-23			ENSG00000182974	ENSG00000182974		"""GPCR / Class A : Olfactory receptors"""	15373	protein-coding gene	gene with protein product							Standard	NM_001004719		Approved		uc010tzu.2	Q8NGB6	OTTHUMG00000171738	ENST00000332663.2:c.851G>A	15.37:g.22369426G>A	ENSP00000329467:p.Arg284His	Somatic	339	2	0.0058997		WXS	Illumina HiSeq	Phase_I	330	7	0.0212121	NM_001004719	B9EH16|Q6IEY2	Missense_Mutation	SNP	ENST00000332663.2	37	CCDS32172.1	1107	0.5068681318681318	216	0.43902439024390244	227	0.6270718232044199	253	0.4423076923076923	411	0.5422163588390502	.	12.82	2.051834	0.36181	0.431003	0.558372	ENSG00000182974	ENST00000332663	T	0.37058	1.22	2.28	2.28	0.28536	GPCR, rhodopsin-like superfamily (1);	0.000000	0.44285	D	0.000472	T	0.00012	0.0000	N	0.08118	0	0.49915	P	1.6799999999994597E-4	B	0.22414	0.069	B	0.09377	0.004	T	0.37033	-0.9723	9	0.87932	D	0	-9.8508	6.6756	0.23092	0.0:0.0:0.2432:0.7568	rs4087943	284	Q8NGB6	OR4M2_HUMAN	H	284	ENSP00000329467:R284H	ENSP00000329467:R284H	R	+	2	0	OR4M2	19870790	0.996000	0.38824	0.998000	0.56505	0.812000	0.45895	5.485000	0.66850	0.148000	0.19059	-0.598000	0.04106	CGT	G|0.493;A|0.507	0.507	strong		0.363	OR4M2-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414921.1		
HELB	92797	hgsc.bcm.edu	37	12	66717784	66717784	+	Silent	SNP	T	T	A	rs35536133	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr12:66717784T>A	ENST00000247815.4	+	10	2378	c.2319T>A	c.(2317-2319)gtT>gtA	p.V773V		NM_033647.3	NP_387467.2	Q8NG08	HELB_HUMAN	helicase (DNA) B	773					DNA duplex unwinding (GO:0032508)|DNA replication (GO:0006260)|DNA replication, synthesis of RNA primer (GO:0006269)		ATP binding (GO:0005524)|ATP-dependent 5'-3' DNA helicase activity (GO:0043141)|single-stranded DNA-dependent ATP-dependent DNA helicase activity (GO:0017116)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(10)|lung(15)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)	40			GBM - Glioblastoma multiforme(2;0.000142)	GBM - Glioblastoma multiforme(28;0.0265)		GTAGACTTGTTTTTGGAATTG	0.343													A|||	655	0.130791	0.2814	0.0375	5008	,	,		17082	0.1498		0.0199	False		,,,				2504	0.0879				p.V773V		Atlas-SNP	.											.	HELB	90	.	0			c.T2319A						PASS	.	A		1029,3377	726.8+/-409.8	126,777,1300	131.0	146.0	141.0		2319	-7.5	0.0	12	dbSNP_126	141	101,8499	814.5+/-407.0	0,101,4199	no	coding-synonymous	HELB	NM_033647.2		126,878,5499	AA,AT,TT		1.1744,23.3545,8.6883		773/1088	66717784	1130,11876	2203	4300	6503	SO:0001819	synonymous_variant	92797	exon10			ACTTGTTTTTGGA	AF319995	CCDS8976.1	12q14.2	2009-01-15			ENSG00000127311	ENSG00000127311			17196	protein-coding gene	gene with protein product		614539				12181327	Standard	NM_033647		Approved		uc001sti.3	Q8NG08	OTTHUMG00000169006	ENST00000247815.4:c.2319T>A	12.37:g.66717784T>A		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	120	7	0.0583333	NM_033647	A8K4C9|Q4G0T2|Q9H7L5	Silent	SNP	ENST00000247815.4	37	CCDS8976.1																																																																																			T|0.913;A|0.087	0.087	strong		0.343	HELB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401919.1		
DNAJC9	23234	hgsc.bcm.edu	37	10	75006804	75006804	+	Silent	SNP	A	A	G	rs35302968	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr10:75006804A>G	ENST00000372950.4	-	1	1816	c.144T>C	c.(142-144)ggT>ggC	p.G48G	MRPS16_ENST00000416782.2_3'UTR|DNAJC9-AS1_ENST00000513954.1_RNA|MRPS16_ENST00000479005.1_5'Flank|DNAJC9-AS1_ENST00000440197.2_RNA	NM_015190.3	NP_056005.1	Q8WXX5	DNJC9_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 9	48	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)					TGTCGCCCTCACCCACCCGGT	0.706													G|||	1158	0.23123	0.351	0.1239	5008	,	,		10508	0.3105		0.0636	False		,,,				2504	0.2362				p.G48G		Atlas-SNP	.											.	DNAJC9	19	.	0			c.T144C						PASS	.	G		1190,3186		166,858,1164	11.0	11.0	11.0		144	1.0	1.0	10	dbSNP_126	11	551,8003		24,503,3750	no	coding-synonymous	DNAJC9	NM_015190.3		190,1361,4914	GG,GA,AA		6.4414,27.1938,13.4648		48/261	75006804	1741,11189	2188	4277	6465	SO:0001819	synonymous_variant	23234	exon1			GCCCTCACCCACC	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.144T>C	10.37:g.75006804A>G		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	117	7	0.0598291	NM_015190	B2RMW6	Silent	SNP	ENST00000372950.4	37	CCDS7322.1																																																																																			A|0.827;G|0.173	0.173	strong		0.706	DNAJC9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048643.1	NM_015190	
GIGYF2	26058	hgsc.bcm.edu	37	2	233659553	233659553	+	Missense_Mutation	SNP	C	C	A	rs2289912	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr2:233659553C>A	ENST00000409547.1	+	15	1689	c.1378C>A	c.(1378-1380)Cct>Act	p.P460T	GIGYF2_ENST00000409196.3_Missense_Mutation_p.P454T|GIGYF2_ENST00000409451.3_Missense_Mutation_p.P481T|GIGYF2_ENST00000452341.2_Missense_Mutation_p.P291T|GIGYF2_ENST00000373563.4_Missense_Mutation_p.P460T|GIGYF2_ENST00000409480.1_Missense_Mutation_p.P482T|GIGYF2_ENST00000373566.3_Missense_Mutation_p.P482T	NM_015575.3	NP_056390.2	Q6Y7W6	PERQ2_HUMAN	GRB10 interacting GYF protein 2	460	Pro-rich.		P -> T (in dbSNP:rs2289912). {ECO:0000269|PubMed:18358451}.		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)	p.P460T(1)		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)		CAATCCTAGTCCTACTCTCCG	0.502													C|||	416	0.0830671	0.0113	0.0634	5008	,	,		18798	0.2302		0.0318	False		,,,				2504	0.0951				p.P481T		Atlas-SNP	.											GIGYF2,NS,carcinoma,0,1	GIGYF2	288	1	1	Substitution - Missense(1)	stomach(1)	c.C1441A						PASS	.	C	THR/PRO,THR/PRO,THR/PRO,THR/PRO	33,4373	37.6+/-69.7	0,33,2170	259.0	260.0	260.0		1378,1360,1441,1378	3.0	1.0	2	dbSNP_100	260	170,8430	79.2+/-141.9	3,164,4133	yes	missense,missense,missense,missense	GIGYF2	NM_015575.3,NM_001103148.1,NM_001103147.1,NM_001103146.1	38,38,38,38	3,197,6303	AA,AC,CC		1.9767,0.749,1.5608	benign,benign,benign,benign	460/1300,454/1294,481/1321,460/1300	233659553	203,12803	2203	4300	6503	SO:0001583	missense	26058	exon15			CCTAGTCCTACTC	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.1378C>A	2.37:g.233659553C>A	ENSP00000386537:p.Pro460Thr	Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	132	8	0.0606061	NM_001103147	A6H8W4|B9EG55|E9PBB0|O75137|Q7Z2Z8|Q7Z3I2|Q96HU4|Q9NV82	Missense_Mutation	SNP	ENST00000409547.1	37	CCDS33401.1	196	0.08974358974358974	10	0.02032520325203252	20	0.055248618784530384	142	0.24825174825174826	24	0.0316622691292876	C	11.37	1.618104	0.28801	0.00749	0.019767	ENSG00000204120	ENST00000373566;ENST00000414511;ENST00000373563;ENST00000409480;ENST00000409547;ENST00000535418;ENST00000423659;ENST00000409196;ENST00000409451;ENST00000440945;ENST00000452341	T;T;T;T;T;T;T;T;T	0.74632	-0.7;-0.7;-0.7;-0.7;-0.86;-0.69;-0.7;-0.83;-0.55	4.83	2.97	0.34412	.	0.333020	0.31897	N	0.006890	T	0.00039	0.0001	L	0.48362	1.52	0.28878	P	0.894564	P;P;B;P	0.41597	0.519;0.756;0.012;0.664	B;B;B;B	0.39339	0.269;0.297;0.023;0.164	T	0.09271	-1.0682	9	0.14252	T	0.57	-4.2104	5.0707	0.14606	0.0:0.5982:0.154:0.2478	rs2289912;rs52825380;rs2289912	291;481;460;454	E9PC50;A6H8W4;Q6Y7W6;E9PBB0	.;.;PERQ2_HUMAN;.	T	482;403;460;482;460;460;403;454;481;454;291	ENSP00000362667:P482T;ENSP00000362664:P460T;ENSP00000386765:P482T;ENSP00000386537:P460T;ENSP00000404195:P403T;ENSP00000387070:P454T;ENSP00000387170:P481T;ENSP00000410297:P454T;ENSP00000411505:P291T	ENSP00000362664:P460T	P	+	1	0	GIGYF2	233367797	1.000000	0.71417	0.997000	0.53966	0.989000	0.77384	1.594000	0.36697	0.524000	0.28502	0.563000	0.77884	CCT	C|0.950;A|0.050	0.050	strong		0.502	GIGYF2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000330316.2	NM_001103146	
OR51G1	79324	hgsc.bcm.edu	37	11	4945196	4945196	+	Missense_Mutation	SNP	T	T	G	rs1378739	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr11:4945196T>G	ENST00000321961.2	-	1	441	c.374A>C	c.(373-375)tAc>tCc	p.Y125S	MMP26_ENST00000477339.1_Intron|MMP26_ENST00000380390.1_Intron	NM_001005237.1	NP_001005237.1	Q8NGK1	O51G1_HUMAN	olfactory receptor, family 51, subfamily G, member 1	125			Y -> S (in dbSNP:rs1378739). {ECO:0000269|PubMed:15489334}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|endometrium(1)|large_intestine(2)|lung(11)|ovary(2)|prostate(3)|skin(4)|soft_tissue(1)	25		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;2.58e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0284)|LUSC - Lung squamous cell carcinoma(625;0.19)		GACGGCCACGTAGCGGTCAAT	0.507													T|||	3292	0.657348	0.7231	0.6484	5008	,	,		22751	0.7222		0.5686	False		,,,				2504	0.5992				p.Y125S		Atlas-SNP	.											.	OR51G1	74	.	0			c.A374C						PASS	.	T	SER/TYR	3078,1324	695.5+/-405.9	1059,960,182	110.0	98.0	102.0		374	3.0	1.0	11	dbSNP_88	102	4985,3611	625.5+/-397.7	1451,2083,764	yes	missense	OR51G1	NM_001005237.1	144	2510,3043,946	GG,GT,TT		42.0079,30.0772,37.9674	probably-damaging	125/322	4945196	8063,4935	2201	4298	6499	SO:0001583	missense	79324	exon1			GCCACGTAGCGGT	AB065793	CCDS31366.1	11p15.4	2012-08-09			ENSG00000176879	ENSG00000176879		"""GPCR / Class A : Olfactory receptors"""	14738	protein-coding gene	gene with protein product				OR51G3P			Standard	NM_001005237		Approved		uc010qyr.2	Q8NGK1	OTTHUMG00000066532	ENST00000321961.2:c.374A>C	11.37:g.4945196T>G	ENSP00000322546:p.Tyr125Ser	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	96	5	0.0520833	NM_001005237	B9EGW8|Q6IFH6	Missense_Mutation	SNP	ENST00000321961.2	37	CCDS31366.1	1442	0.6602564102564102	372	0.7560975609756098	244	0.6740331491712708	410	0.7167832167832168	416	0.5488126649076517	T	9.340	1.062863	0.19987	0.699228	0.579921	ENSG00000176879	ENST00000321961	T	0.57436	0.4	4.2	2.99	0.34606	GPCR, rhodopsin-like superfamily (1);	0.227317	0.22524	U	0.058922	T	0.00012	0.0000	M	0.86953	2.85	0.30227	P	0.796256	P	0.41748	0.761	B	0.37346	0.247	T	0.38542	-0.9656	9	0.87932	D	0	.	9.0162	0.36170	0.1644:0.0:0.0:0.8356	rs1378739;rs17337943	125	Q8NGK1	O51G1_HUMAN	S	125	ENSP00000322546:Y125S	ENSP00000322546:Y125S	Y	-	2	0	OR51G1	4901772	0.085000	0.21516	0.996000	0.52242	0.061000	0.15899	0.375000	0.20518	1.760000	0.52011	0.455000	0.32223	TAC	T|0.355;G|0.645	0.645	strong		0.507	OR51G1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142345.1	NM_001005237	
HLA-DRB5	3127	hgsc.bcm.edu	37	6	32489749	32489749	+	Silent	SNP	G	G	C	rs1064594		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr6:32489749G>C	ENST00000374975.3	-	2	365	c.303C>G	c.(301-303)cgC>cgG	p.R101R		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						CCACCGCGGCGCGCCTGTCTT	0.662																																					p.R101R		Atlas-SNP	.											.	HLA-DRB5	31	.	0			c.C303G						PASS	.	C		2544,1408		1175,194,607	33.0	29.0	30.0		303	-1.5	0.0	6	dbSNP_86	30	5096,2670		2414,268,1201	no	coding-synonymous	HLA-DRB5	NM_002125.3		3589,462,1808	CC,CG,GG		34.3806,35.6275,34.8012		101/267	32489749	7640,4078	1976	3883	5859	SO:0001819	synonymous_variant	3127	exon2			CGCGGCGCGCCTG		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.303C>G	6.37:g.32489749G>C		Somatic	0	0	.		WXS	Illumina HiSeq	Phase_I	5	5	1	NM_002125		Silent	SNP	ENST00000374975.3	37	CCDS4751.1																																																																																			G|0.339;C|0.661	0.661	strong		0.662	HLA-DRB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076022.2	NM_002125	
MLPH	79083	hgsc.bcm.edu	37	2	238443226	238443226	+	Missense_Mutation	SNP	A	A	G	rs2292884	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr2:238443226A>G	ENST00000264605.3	+	9	1334	c.1040A>G	c.(1039-1041)cAt>cGt	p.H347R	MLPH_ENST00000445024.2_Missense_Mutation_p.H347R|MLPH_ENST00000338530.4_Intron|MLPH_ENST00000409373.1_Intron|MLPH_ENST00000468178.1_Intron|MLPH_ENST00000410032.1_Intron	NM_024101.5	NP_077006.1	Q9BV36	MELPH_HUMAN	melanophilin	347			H -> R (in dbSNP:rs2292884).		melanocyte differentiation (GO:0030318)|melanosome localization (GO:0032400)|protein targeting (GO:0006605)	cortical actin cytoskeleton (GO:0030864)|extracellular vesicular exosome (GO:0070062)|microtubule organizing center (GO:0005815)|microtubule plus-end (GO:0035371)|stress fiber (GO:0001725)	metal ion binding (GO:0046872)			NS(1)|breast(3)|cervix(1)|endometrium(3)|large_intestine(2)|lung(11)|ovary(1)|stomach(2)|upper_aerodigestive_tract(1)	25		Breast(86;0.000381)|Renal(207;0.000966)|Ovarian(221;0.0695)|all_hematologic(139;0.095)|all_lung(227;0.17)|Melanoma(123;0.203)		Epithelial(121;1.17e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.02e-10)|Kidney(56;4.23e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.15e-07)|BRCA - Breast invasive adenocarcinoma(100;0.000439)|Lung(119;0.0132)|LUSC - Lung squamous cell carcinoma(224;0.0316)		CTGAATAAGCATATTTCAGCT	0.552													G|||	1860	0.371406	0.621	0.3098	5008	,	,		20283	0.2748		0.2097	False		,,,				2504	0.3436				p.H347R		Atlas-SNP	.											.	MLPH	41	.	0			c.A1040G						PASS	.	G	,ARG/HIS	2503,1903	545.1+/-376.7	712,1079,412	132.0	126.0	128.0	http://www.ncbi.nlm.nih.gov/pubmed?term	,1040	0.0	0.0	2	dbSNP_100	128	2189,6411	711.9+/-405.9	269,1651,2380	yes	intron,missense	MLPH	NM_001042467.1,NM_024101.5	,29	981,2730,2792	GG,GA,AA	http://www.ncbi.nlm.nih.gov/pubmed?term	25.4535,43.1911,36.0757	,benign	,347/601	238443226	4692,8314	2203	4300	6503	SO:0001583	missense	79083	exon9			ATAAGCATATTTC	AY358857	CCDS2518.1, CCDS42836.1, CCDS63172.1, CCDS63173.1	2q37.2	2014-09-17			ENSG00000115648	ENSG00000115648			29643	protein-coding gene	gene with protein product		606526				11980908, 11504925	Standard	NM_024101		Approved	l1Rk3, l(1)-3Rk, Slac-2a, ln, exophilin-3	uc002vwt.3	Q9BV36	OTTHUMG00000133298	ENST00000264605.3:c.1040A>G	2.37:g.238443226A>G	ENSP00000264605:p.His347Arg	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	120	7	0.0583333	NM_024101	B3KSS2|B4DKW7|G5E9G5|Q9HA71	Missense_Mutation	SNP	ENST00000264605.3	37	CCDS2518.1	723	0.33104395604395603	305	0.6199186991869918	98	0.27071823204419887	159	0.27797202797202797	161	0.21240105540897097	G	0.005	-2.149150	0.00328	0.568089	0.254535	ENSG00000115648	ENST00000264605;ENST00000445024;ENST00000437893	T;T;T	0.14144	3.1;3.01;2.53	3.99	0.0132	0.14094	.	0.873451	0.09484	N	0.795883	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.43015	-0.9417	9	0.02654	T	1	-1.4822	8.7039	0.34343	0.4573:0.0:0.5427:0.0	rs2292884;rs11539362;rs60898014;rs2292884	8;347	Q53QV8;Q9BV36	.;MELPH_HUMAN	R	347;347;107	ENSP00000264605:H347R;ENSP00000414849:H347R;ENSP00000412438:H107R	ENSP00000264605:H347R	H	+	2	0	MLPH	238107965	0.000000	0.05858	0.000000	0.03702	0.557000	0.35523	0.241000	0.18065	-0.177000	0.10690	-0.119000	0.15052	CAT	A|0.644;G|0.356	0.356	strong		0.552	MLPH-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257083.2	NM_024101	
ATP8A2	51761	hgsc.bcm.edu	37	13	26043182	26043182	+	Silent	SNP	A	A	C	rs7317185	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr13:26043182A>C	ENST00000381655.2	+	2	286	c.144A>C	c.(142-144)ggA>ggC	p.G48G	ATP8A2_ENST00000255283.8_Silent_p.G8G	NM_016529.4	NP_057613.4	Q9NTI2	AT8A2_HUMAN	ATPase, aminophospholipid transporter, class I, type 8A, member 2	8					aging (GO:0007568)|axonogenesis (GO:0007409)|detection of light stimulus involved in visual perception (GO:0050908)|eating behavior (GO:0042755)|inner ear morphogenesis (GO:0042472)|involuntary skeletal muscle contraction (GO:0003011)|negative regulation of cell proliferation (GO:0008285)|neurofilament cytoskeleton organization (GO:0060052)|neuromuscular process controlling posture (GO:0050884)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of neuron projection development (GO:0010976)|positive regulation of phospholipid translocation (GO:0061092)|response to auditory stimulus (GO:0010996)|retina layer formation (GO:0010842)|skin development (GO:0043588)	cell projection (GO:0042995)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(17)|lung(31)|ovary(4)|skin(3)|stomach(1)|urinary_tract(1)	72		Breast(139;0.0201)|Lung SC(185;0.0225)		all cancers(112;0.043)|OV - Ovarian serous cystadenocarcinoma(117;0.0748)|Epithelial(112;0.079)		CGTCTGTTGGAGACCAGCTGG	0.582													A|||	1022	0.204073	0.354	0.1484	5008	,	,		9431	0.119		0.1998	False		,,,				2504	0.1329				p.G48G		Atlas-SNP	.											ATP8A2,colon,carcinoma,0,1	ATP8A2	181	1	0			c.A144C						scavenged	.	A		1226,2880		185,856,1012	77.0	86.0	83.0		144	0.1	1.0	13	dbSNP_116	83	1789,6605		191,1407,2599	no	coding-synonymous	ATP8A2	NM_016529.4		376,2263,3611	CC,CA,AA		21.3128,29.8587,24.12		48/1189	26043182	3015,9485	2053	4197	6250	SO:0001819	synonymous_variant	51761	exon2			TGTTGGAGACCAG	AL137256	CCDS41873.1	13q12	2010-04-20	2010-03-31		ENSG00000132932	ENSG00000132932	3.6.3.1	"""ATPases / P-type"""	13533	protein-coding gene	gene with protein product		605870	"""ATPase, aminophospholipid transporter-like, Class I, type 8A, member 2"", ""ATPase, aminophospholipid transporter-like, class I, type 8A, member 2"""			11015572, 19778899	Standard	NM_016529		Approved	ATPIB, ML-1	uc001uqk.3	Q9NTI2	OTTHUMG00000016611	ENST00000381655.2:c.144A>C	13.37:g.26043182A>C		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	81	4	0.0493827	NM_016529	Q9H527|Q9NPU6|Q9NTL2|Q9NYM3	Silent	SNP	ENST00000381655.2	37	CCDS41873.1	455	0.20833333333333334	166	0.33739837398373984	68	0.1878453038674033	75	0.13111888111888112	146	0.19261213720316622	A	12.71	2.020365	0.35606	0.298587	0.213128	ENSG00000132932	ENST00000544544	.	.	.	4.16	0.119	0.14685	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.42310	-0.9459	4	0.11485	T	0.65	.	0.3655	0.00371	0.3332:0.1995:0.2735:0.1938	rs7317185;rs7317185	.	.	.	A	10	.	ENSP00000444329:E10A	E	+	2	0	ATP8A2	24941182	1.000000	0.71417	0.999000	0.59377	0.994000	0.84299	1.074000	0.30703	0.144000	0.18951	0.329000	0.21502	GAG	A|0.790;C|0.210	0.210	strong		0.582	ATP8A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044236.2	NM_016529	
UBB	7314	hgsc.bcm.edu	37	17	16285542	16285542	+	Silent	SNP	G	G	A	rs17052364	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr17:16285542G>A	ENST00000395837.1	+	2	502	c.321G>A	c.(319-321)caG>caA	p.Q107Q	UBB_ENST00000302182.3_Silent_p.Q107Q|RP11-138I1.4_ENST00000583934.1_RNA|UBB_ENST00000578649.1_Intron|UBB_ENST00000395839.1_Silent_p.Q107Q|UBB_ENST00000535788.1_Intron	NM_001281718.1|NM_001281720.1	NP_001268647.1|NP_001268649.1	P0CG47	UBB_HUMAN	ubiquitin B	107	Ubiquitin-like 2. {ECO:0000255|PROSITE- ProRule:PRU00214}.		GMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQ QRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFV KTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFA GKQLEDGRTLSDYNIQKESTLHLVLRLRGGC -> YADLRE DPDRQDHHPGSGAQ (in UBB(+1); loss of polyubiquitination; impairs the ubiquitin-proteasome pathway; refractory to disassembly by DUBs; slow degradation by UCHL3).		activation of MAPK activity (GO:0000187)|anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|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 peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|carbohydrate metabolic process (GO:0005975)|cellular response to hypoxia (GO:0071456)|cytokine-mediated signaling pathway (GO:0019221)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|endosomal transport (GO:0016197)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|gene expression (GO:0010467)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|innate immune response (GO:0045087)|intracellular transport of virus (GO:0075733)|ion transmembrane transport (GO:0034220)|JNK cascade (GO:0007254)|membrane organization (GO:0061024)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|negative regulation of type I interferon production (GO:0032480)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of apoptotic process (GO:0043065)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of type I interferon production (GO:0032479)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|stress-activated MAPK cascade (GO:0051403)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|transmembrane transport (GO:0055085)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral protein processing (GO:0019082)|virion assembly (GO:0019068)	cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)		p.Q107Q(1)		breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	16				UCEC - Uterine corpus endometrioid carcinoma (92;0.0822)		CCAAGATCCAGGATAAAGAAG	0.537																																					p.Q107Q	Melanoma(163;1126 3406 34901)	Atlas-SNP	.											UBB,NS,carcinoma,0,1	UBB	30	1	1	Substitution - coding silent(1)	lung(1)	c.G321A						scavenged	.						114.0	110.0	112.0					17																	16285542		2203	4300	6503	SO:0001819	synonymous_variant	7314	exon2			GATCCAGGATAAA		CCDS11177.1	17p12-p11.2	2010-11-25			ENSG00000170315	ENSG00000170315			12463	protein-coding gene	gene with protein product	"""polyubiquitin B"""	191339				2154095	Standard	NM_018955		Approved	MGC8385, FLJ25987	uc002gpx.3	P0CG47	OTTHUMG00000058987	ENST00000395837.1:c.321G>A	17.37:g.16285542G>A		Somatic	238	1	0.00420168		WXS	Illumina HiSeq	Phase_I	245	4	0.0163265	NM_018955	P02248|P02249|P02250|P62988|Q29120|Q6LBL4|Q6LDU5|Q8WYN8|Q91887|Q91888|Q9BWD6|Q9BX98|Q9UEF2|Q9UEG1|Q9UEK8|Q9UPK7	Silent	SNP	ENST00000395837.1	37	CCDS11177.1																																																																																			G|0.540;A|0.460	0.460	strong		0.537	UBB-002	NOVEL	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000130459.1	NM_018955	
CFAP70	118491	hgsc.bcm.edu	37	10	75035257	75035257	+	Missense_Mutation	SNP	T	T	C	rs4294502	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr10:75035257T>C	ENST00000310715.3	-	23	2950	c.2830A>G	c.(2830-2832)Aac>Gac	p.N944D	TTC18_ENST00000340329.3_Intron|TTC18_ENST00000493787.1_5'UTR|TTC18_ENST00000394865.1_Missense_Mutation_p.N944D|TTC18_ENST00000355577.3_Missense_Mutation_p.N413D|DNAJC9-AS1_ENST00000440197.2_RNA|TTC18_ENST00000401621.2_Missense_Mutation_p.N944D	NM_145170.3	NP_660153.3	Q5T0N1	TTC18_HUMAN		944			N -> D (in dbSNP:rs4294502).			extracellular vesicular exosome (GO:0070062)		p.N944D(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(13)|ovary(2)|prostate(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	34	Prostate(51;0.0119)					TTGGCAAAGTTCTTCTTAAGA	0.478													C|||	1149	0.229433	0.3525	0.1239	5008	,	,		18523	0.3105		0.0636	False		,,,				2504	0.2249				p.N944D		Atlas-SNP	.											TTC18,NS,carcinoma,0,1	TTC18	106	1	1	Substitution - Missense(1)	stomach(1)	c.A2830G						PASS	.	C	ASP/ASN	1382,3024	689.1+/-405.1	214,954,1035	226.0	213.0	217.0		2830	5.9	1.0	10	dbSNP_111	217	618,7982	791.7+/-407.5	31,556,3713	yes	missense	TTC18	NM_145170.3	23	245,1510,4748	CC,CT,TT		7.186,31.3663,15.3775	benign	944/1122	75035257	2000,11006	2203	4300	6503	SO:0001583	missense	118491	exon23			CAAAGTTCTTCTT																												ENST00000310715.3:c.2830A>G	10.37:g.75035257T>C	ENSP00000310829:p.Asn944Asp	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	138	7	0.0507246	NM_145170	C9JIZ9|Q5T0M4|Q5T0M9|Q5T0N0|Q69YH9|Q8IYZ8|Q8N7D5|Q8NI30|Q8NI31	Missense_Mutation	SNP	ENST00000310715.3	37	CCDS7324.3	457	0.20924908424908426	187	0.3800813008130081	40	0.11049723756906077	183	0.31993006993006995	47	0.06200527704485488	C	7.528	0.658154	0.14645	0.313663	0.07186	ENSG00000156042	ENST00000310715;ENST00000401621;ENST00000355577;ENST00000433268;ENST00000394865	T;T;T;T	0.62105	0.05;0.05;0.34;0.34	5.87	5.87	0.94306	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.109437	0.64402	N	0.000010	T	0.00012	0.0000	N	0.01874	-0.695	0.54753	P	1.4999999999987246E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.17107	-1.0380	9	0.02654	T	1	-2.9252	13.0531	0.58966	0.0:0.9225:0.0:0.0775	rs4294502;rs52829733;rs61409923;rs4294502	944	Q5T0N1	TTC18_HUMAN	D	944;944;944;351;944	ENSP00000310829:N944D;ENSP00000384479:N944D;ENSP00000409527:N351D;ENSP00000378334:N944D	ENSP00000310829:N944D	N	-	1	0	TTC18	74705263	1.000000	0.71417	1.000000	0.80357	0.777000	0.43975	2.353000	0.44089	1.510000	0.48803	-0.119000	0.15052	AAC	T|0.811;C|0.189	0.189	strong		0.478	TTC18-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding			
PREX1	57580	hgsc.bcm.edu	37	20	47246077	47246077	+	Missense_Mutation	SNP	C	C	G	rs3936192	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr20:47246077C>G	ENST00000371941.3	-	37	4698	c.4676G>C	c.(4675-4677)aGt>aCt	p.S1559T	PREX1_ENST00000396220.1_3'UTR	NM_020820.3	NP_065871	Q8TCU6	PREX1_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 1	1559			S -> T (in dbSNP:rs3936192).		actin filament polymerization (GO:0030041)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|neutrophil activation (GO:0042119)|neutrophil chemotaxis (GO:0030593)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|regulation of actin filament polymerization (GO:0030833)|regulation of dendrite development (GO:0050773)|superoxide metabolic process (GO:0006801)|T cell differentiation (GO:0030217)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|growth cone (GO:0030426)|intracellular membrane-bounded organelle (GO:0043231)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|phospholipid binding (GO:0005543)|Rho GTPase activator activity (GO:0005100)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|central_nervous_system(1)|endometrium(4)|kidney(6)|large_intestine(27)|lung(53)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|stomach(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	110			BRCA - Breast invasive adenocarcinoma(12;0.0135)|Colorectal(8;0.198)			GGCGCCCACACTCCCAGCAGC	0.632													C|||	627	0.1252	0.0446	0.147	5008	,	,		17135	0.1597		0.1054	False		,,,				2504	0.2035				p.S1559T		Atlas-SNP	.											.	PREX1	441	.	0			c.G4676C						PASS	.	C	THR/SER	222,4184	134.9+/-171.1	6,210,1987	78.0	82.0	80.0		4676	1.8	0.2	20	dbSNP_108	80	811,7789	188.4+/-235.4	35,741,3524	yes	missense	PREX1	NM_020820.3	58	41,951,5511	GG,GC,CC		9.4302,5.0386,7.9425	benign	1559/1660	47246077	1033,11973	2203	4300	6503	SO:0001583	missense	57580	exon37			CCCACACTCCCAG	AB037836	CCDS13410.1	20q13.13	2013-01-10	2008-09-15		ENSG00000124126	ENSG00000124126		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	32594	protein-coding gene	gene with protein product		606905				11955434, 15545267, 16301320	Standard	NM_020820		Approved	KIAA1415, P-REX1	uc002xtw.1	Q8TCU6	OTTHUMG00000032685	ENST00000371941.3:c.4676G>C	20.37:g.47246077C>G	ENSP00000361009:p.Ser1559Thr	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	111	5	0.045045	NM_020820	E1P5X9|Q5JS95|Q5JS96|Q69YL2|Q7Z2L9|Q9BQH0|Q9BX55|Q9H4Q6|Q9P2D2|Q9UGQ4	Missense_Mutation	SNP	ENST00000371941.3	37	CCDS13410.1	267	0.12225274725274725	34	0.06910569105691057	49	0.13535911602209943	101	0.17657342657342656	83	0.10949868073878628	C	0.861	-0.735145	0.03111	0.050386	0.094302	ENSG00000124126	ENST00000371941	T	0.61859	0.07	3.95	1.8	0.24995	.	0.642949	0.13848	U	0.358568	T	0.00039	0.0001	N	0.01048	-1.04	0.58432	P	1.0000000000287557E-6	B;B	0.32051	0.354;0.006	B;B	0.27887	0.084;0.007	T	0.10405	-1.0631	9	0.20519	T	0.43	.	4.2811	0.10833	0.1196:0.4991:0.2805:0.1008	rs3936192;rs3936192	1559;856	Q8TCU6;Q8TCU6-2	PREX1_HUMAN;.	T	1559	ENSP00000361009:S1559T	ENSP00000361009:S1559T	S	-	2	0	PREX1	46679484	0.860000	0.29831	0.151000	0.22473	0.119000	0.20118	1.854000	0.39368	0.777000	0.33496	0.462000	0.41574	AGT	C|0.908;G|0.092	0.092	strong		0.632	PREX1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079623.1	NM_020820	
VPS41	27072	hgsc.bcm.edu	37	7	38796570	38796570	+	Silent	SNP	G	G	A	rs2240350	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr7:38796570G>A	ENST00000310301.4	-	19	1617	c.1563C>T	c.(1561-1563)gaC>gaT	p.D521D	VPS41_ENST00000395969.2_Silent_p.D496D	NM_014396.3	NP_055211.2	P49754	VPS41_HUMAN	vacuolar protein sorting 41 homolog (S. cerevisiae)	521					Golgi vesicle transport (GO:0048193)|intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	cytosol (GO:0005829)|early endosome (GO:0005769)|Golgi-associated vesicle (GO:0005798)|HOPS complex (GO:0030897)|late endosome (GO:0005770)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)	zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(5)|kidney(4)|large_intestine(5)|lung(17)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(4)	44						CATAGTTCTTGTCATAGGTGT	0.299													G|||	1794	0.358227	0.2549	0.5965	5008	,	,		16905	0.4206		0.3469	False		,,,				2504	0.2761				p.D521D		Atlas-SNP	.											.	VPS41	102	.	0			c.C1563T						PASS	.	G	,	1278,3126	433.5+/-343.6	186,906,1110	103.0	106.0	105.0		1563,1488	4.1	1.0	7	dbSNP_98	105	3076,5516	469.7+/-367.6	510,2056,1730	no	coding-synonymous,coding-synonymous	VPS41	NM_014396.3,NM_080631.3	,	696,2962,2840	AA,AG,GG		35.8007,29.0191,33.5026	,	521/855,496/830	38796570	4354,8642	2202	4296	6498	SO:0001819	synonymous_variant	27072	exon19			GTTCTTGTCATAG	U87309	CCDS5457.1, CCDS5458.2	7p14.1-p13	2009-05-08	2006-12-19		ENSG00000006715	ENSG00000006715			12713	protein-coding gene	gene with protein product		605485	"""vacuolar protein sorting 41 (yeast homolog)"", ""vacuolar protein sorting 41 (yeast)"""			9159129	Standard	NM_080631		Approved	HVSP41	uc003tgy.3	P49754	OTTHUMG00000023629	ENST00000310301.4:c.1563C>T	7.37:g.38796570G>A		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	109	5	0.0458716	NM_014396	E9PF36|Q86TP8|Q99851|Q99852	Silent	SNP	ENST00000310301.4	37	CCDS5457.1																																																																																			G|0.643;A|0.357	0.357	strong		0.299	VPS41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226986.3		
CENPC	1060	hgsc.bcm.edu	37	4	68384008	68384008	+	Silent	SNP	C	C	T	rs355510	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr4:68384008C>T	ENST00000273853.6	-	7	946	c.696G>A	c.(694-696)tcG>tcA	p.S232S		NM_001812.2	NP_001803.2	Q03188	CENPC_HUMAN	centromere protein C	232					chromosome segregation (GO:0007059)|kinetochore assembly (GO:0051382)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	condensed nuclear chromosome, centromeric region (GO:0000780)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|nucleus (GO:0005634)|pericentric heterochromatin (GO:0005721)	centromeric DNA binding (GO:0019237)|DNA binding (GO:0003677)										CTTGTCCTTCCGATGTTTTAT	0.294													T|||	3527	0.704273	0.6316	0.7565	5008	,	,		15873	0.8274		0.6252	False		,,,				2504	0.7198				p.S232S		Atlas-SNP	.											.	CENPC1	66	.	0			c.G696A						PASS	.	T		2265,1305		744,777,264	48.0	42.0	43.0		696	1.2	0.0	4	dbSNP_79	43	4795,3291		1461,1873,709	no	coding-synonymous	CENPC1	NM_001812.2		2205,2650,973	TT,TC,CC		40.7,36.5546,39.4303		232/944	68384008	7060,4596	1785	4043	5828	SO:0001819	synonymous_variant	1060	exon7			TCCTTCCGATGTT	M95724	CCDS47063.1	4q13.2	2013-11-05	2013-07-03	2013-07-03	ENSG00000145241	ENSG00000145241			1854	protein-coding gene	gene with protein product		117141	"""centromere protein C 1"""	CENPC1		7959789	Standard	XR_245245		Approved	CENP-C, hcp-4, MIF2	uc003hdd.1	Q03188	OTTHUMG00000160735	ENST00000273853.6:c.696G>A	4.37:g.68384008C>T		Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	155	7	0.0451613	NM_001812	Q8IW27|Q9P0M5	Silent	SNP	ENST00000273853.6	37	CCDS47063.1																																																																																			C|0.352;T|0.648	0.648	strong		0.294	CENPC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362001.2		
MUC2	4583	hgsc.bcm.edu	37	11	1093008	1093008	+	Silent	SNP	C	C	T			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr11:1093008C>T	ENST00000441003.2	+	30	4854	c.4827C>T	c.(4825-4827)atC>atT	p.I1609I	MUC2_ENST00000333592.6_5'Flank|MUC2_ENST00000359061.5_Intron|MUC2_ENST00000361558.6_Intron	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)	cgacacccatcaccaccacca	0.627																																					p.I1609I		Atlas-SNP	.											MUC2_ENST00000441003,colon,carcinoma,0,2	MUC2	614	2	0			c.C4827T						scavenged	.						60.0	103.0	88.0					11																	1093008		1815	3369	5184	SO:0001819	synonymous_variant	4583	exon30			ACCCATCACCACC	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.4827C>T	11.37:g.1093008C>T		Somatic	46	5	0.108696		WXS	Illumina HiSeq	Phase_I	60	6	0.1	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	
APEH	327	hgsc.bcm.edu	37	3	49723141	49723141	+	IGR	SNP	A	A	G	rs144982232	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr3:49723141A>G	ENST00000296456.5	+	0	3220				AC099668.5_ENST00000563780.1_RNA|MST1_ENST00000449682.2_Silent_p.H425H|MST1_ENST00000494828.2_5'Flank|MST1_ENST00000383728.3_3'UTR	NM_001640.3	NP_001631.3	P13798	ACPH_HUMAN	acylaminoacyl-peptide hydrolase						beta-amyloid metabolic process (GO:0050435)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear membrane (GO:0031965)	omega peptidase activity (GO:0008242)|poly(A) RNA binding (GO:0044822)|serine-type endopeptidase activity (GO:0004252)			endometrium(3)|large_intestine(1)|lung(6)|ovary(1)|skin(1)|stomach(2)|urinary_tract(1)	15				BRCA - Breast invasive adenocarcinoma(193;4.53e-05)|Kidney(197;0.00218)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)		CCAGTTGTGCATGCGGTTCGG	0.577													A|||	48	0.00958466	0.0	0.0014	5008	,	,		19851	0.0446		0.0	False		,,,				2504	0.002				p.H425H		Atlas-SNP	.											.	MST1	84	.	0			c.T1275C						PASS	.						46.0	45.0	45.0					3																	49723141		2203	4299	6502	SO:0001628	intergenic_variant	4485	exon11			TTGTGCATGCGGT	D38441	CCDS2801.1	3p21	2013-05-29	2013-05-29		ENSG00000164062	ENSG00000164062	3.4.19.1		586	protein-coding gene	gene with protein product	"""acylaminoacyl-peptidase"""	102645	"""N-acylaminoacyl-peptide hydrolase"""	D3F15S2, DNF15S2, D3S48E		2392324	Standard	NM_001640		Approved		uc003cxf.3	P13798	OTTHUMG00000156882		3.37:g.49723141A>G		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	130	6	0.0461538	NM_020998	Q9BQ33|Q9P0Y2	Silent	SNP	ENST00000296456.5	37	CCDS2801.1																																																																																			A|0.989;G|0.011	0.011	strong		0.577	APEH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346415.2		
SMC1B	27127	hgsc.bcm.edu	37	22	45767391	45767391	+	Missense_Mutation	SNP	C	C	T	rs9614653	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr22:45767391C>T	ENST00000357450.4	-	14	2272	c.2273G>A	c.(2272-2274)cGa>cAa	p.R758Q	SMC1B_ENST00000404354.3_Missense_Mutation_p.R758Q	NM_148674.3	NP_683515.3	Q8NDV3	SMC1B_HUMAN	structural maintenance of chromosomes 1B	758			R -> Q (in dbSNP:rs9614653).		meiotic nuclear division (GO:0007126)|sister chromatid cohesion (GO:0007062)	chromosome, centromeric region (GO:0000775)|lateral element (GO:0000800)|meiotic cohesin complex (GO:0030893)|nuclear meiotic cohesin complex (GO:0034991)	ATP binding (GO:0005524)|DNA binding (GO:0003677)	p.R758Q(1)		breast(2)|endometrium(4)|kidney(3)|large_intestine(6)|lung(15)|ovary(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	37		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0182)		TCTTCGTTGTCGTTCCTTGAT	0.284													C|||	887	0.177117	0.0212	0.1499	5008	,	,		18826	0.3442		0.1173	False		,,,				2504	0.2965				p.R758Q		Atlas-SNP	.											SMC1B_ENST00000357450,rectum,carcinoma,-1,3	SMC1B	215	3	1	Substitution - Missense(1)	stomach(1)	c.G2273A						scavenged	.	C	GLN/ARG	95,3537		3,89,1724	102.0	93.0	96.0		2273	3.5	1.0	22	dbSNP_119	96	965,7177		60,845,3166	yes	missense	SMC1B	NM_148674.3	43	63,934,4890	TT,TC,CC		11.8521,2.6156,9.0029	benign	758/1236	45767391	1060,10714	1816	4071	5887	SO:0001583	missense	27127	exon14			CGTTGTCGTTCCT	AJ504806	CCDS43027.1, CCDS74876.1	22q13	2006-07-06	2006-07-06	2006-07-06	ENSG00000077935	ENSG00000077935		"""Structural maintenance of chromosomes proteins"""	11112	protein-coding gene	gene with protein product		608685	"""SMC1 (structural maintenance of chromosomes 1, yeast)-like 1"", ""SMC1 structural maintenance of chromosomes 1-like 2 (yeast)"""	SMC1L2		10591208, 11564881	Standard	XM_005261566		Approved	bK268H5	uc003bgc.3	Q8NDV3	OTTHUMG00000151334	ENST00000357450.4:c.2273G>A	22.37:g.45767391C>T	ENSP00000350036:p.Arg758Gln	Somatic	176	1	0.00568182		WXS	Illumina HiSeq	Phase_I	158	6	0.0379747	NM_148674	A0AV46|B0QY23|B0QY24|Q5TIC3|Q6ZUF9|Q9Y3G5	Missense_Mutation	SNP	ENST00000357450.4	37	CCDS43027.1	358	0.16391941391941392	13	0.026422764227642278	61	0.1685082872928177	201	0.3513986013986014	83	0.10949868073878628	C	12.91	2.080890	0.36758	0.026156	0.118521	ENSG00000077935	ENST00000357450;ENST00000404354	T;T	0.78924	-1.22;-1.09	5.66	3.51	0.40186	RecF/RecN/SMC (1);	0.228496	0.29995	N	0.010671	T	0.00012	0.0000	L	0.52905	1.665	0.49213	P	2.3799999999996047E-4	B;P;P	0.36789	0.028;0.526;0.57	B;B;B	0.30855	0.094;0.121;0.104	T	0.17289	-1.0374	9	0.18710	T	0.47	.	8.3469	0.32279	0.0:0.8198:0.0:0.1802	rs9614653;rs60966549;rs9614653	758;758;758	Q8NDV3;Q8NDV3-2;Q8NDV3-3	SMC1B_HUMAN;.;.	Q	758	ENSP00000350036:R758Q;ENSP00000385902:R758Q	ENSP00000350036:R758Q	R	-	2	0	SMC1B	44146055	0.855000	0.29742	0.957000	0.39632	0.373000	0.29922	1.456000	0.35201	0.610000	0.30035	0.655000	0.94253	CGA	C|0.845;T|0.155	0.155	strong		0.284	SMC1B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322256.2	NM_148674	
SP1	6667	hgsc.bcm.edu	37	12	53776587	53776587	+	Missense_Mutation	SNP	A	A	G			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr12:53776587A>G	ENST00000327443.4	+	3	954	c.856A>G	c.(856-858)Atc>Gtc	p.I286V	SP1_ENST00000426431.2_Missense_Mutation_p.I279V	NM_001251825.1|NM_138473.2	NP_001238754.1|NP_612482.2	P08047	SP1_HUMAN	Sp1 transcription factor	286	Ser/Thr-rich.|Transactivation domain B (Gln-rich).				cellular lipid metabolic process (GO:0044255)|definitive hemopoiesis (GO:0060216)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic placenta development (GO:0001892)|embryonic process involved in female pregnancy (GO:0060136)|embryonic skeletal system development (GO:0048706)|enucleate erythrocyte differentiation (GO:0043353)|gene expression (GO:0010467)|liver development (GO:0001889)|lung development (GO:0030324)|megakaryocyte differentiation (GO:0030219)|ossification (GO:0001503)|positive regulation by host of viral transcription (GO:0043923)|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)|rhythmic process (GO:0048511)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|trophectodermal cell differentiation (GO:0001829)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein-DNA complex (GO:0032993)	bHLH transcription factor binding (GO:0043425)|core promoter sequence-specific DNA binding (GO:0001046)|DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|enhancer binding (GO:0035326)|histone deacetylase binding (GO:0042826)|HMG box domain binding (GO:0071837)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II repressing transcription factor binding (GO:0001103)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|large_intestine(1)|ovary(1)|skin(1)|stomach(1)	5				BRCA - Breast invasive adenocarcinoma(357;0.00527)		GGCAGTCACGATCAGCAGCTC	0.552																																					p.I286V		Atlas-SNP	.											.	SP1	57	.	0			c.A856G						PASS	.						154.0	137.0	143.0					12																	53776587		2203	4300	6503	SO:0001583	missense	6667	exon3			GTCACGATCAGCA	J03133	CCDS8857.1, CCDS44898.1	12q13.1	2013-01-08						"""Specificity protein transcription factors"", ""Zinc fingers, C2H2-type"""	11205	protein-coding gene	gene with protein product	"""specificity protein 1"""	189906				1662663	Standard	NM_003109		Approved		uc001scw.3	P08047	OTTHUMG00000170047	ENST00000327443.4:c.856A>G	12.37:g.53776587A>G	ENSP00000329357:p.Ile286Val	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	117	6	0.0512821	NM_138473	E4Z9M7|G5E9M8|Q86TN8|Q9H3Q5|Q9NR51|Q9NY21|Q9NYE7	Missense_Mutation	SNP	ENST00000327443.4	37	CCDS8857.1	.	.	.	.	.	.	.	.	.	.	A	7.701	0.693035	0.15039	.	.	ENSG00000185591	ENST00000327443;ENST00000426431	T;T	0.08720	3.09;3.06	4.3	4.3	0.51218	.	0.107759	0.39834	N	0.001248	T	0.03739	0.0106	N	0.08118	0	0.22127	N	0.999343	B	0.06786	0.001	B	0.04013	0.001	T	0.37454	-0.9705	10	0.27785	T	0.31	.	5.2784	0.15663	0.643:0.1818:0.0:0.1751	.	286	P08047	SP1_HUMAN	V	286;279	ENSP00000329357:I286V;ENSP00000404263:I279V	ENSP00000329357:I286V	I	+	1	0	SP1	52062854	0.002000	0.14202	0.981000	0.43875	0.923000	0.55619	0.979000	0.29500	1.943000	0.56356	0.383000	0.25322	ATC	.	.	none		0.552	SP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407044.1		
FAM131C	348487	hgsc.bcm.edu	37	1	16384986	16384986	+	Silent	SNP	G	G	T	rs28496958	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr1:16384986G>T	ENST00000375662.4	-	7	972	c.789C>A	c.(787-789)ctC>ctA	p.L263L	FAM131C_ENST00000494078.1_5'UTR	NM_182623.2	NP_872429.2	Q96AQ9	F131C_HUMAN	family with sequence similarity 131, member C	263	Pro-rich.									large_intestine(2)|lung(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	8		Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Colorectal(212;8.32e-08)|COAD - Colon adenocarcinoma(227;5.56e-06)|BRCA - Breast invasive adenocarcinoma(304;9.12e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.00656)|READ - Rectum adenocarcinoma(331;0.0649)		CCATGGAGGGGAGGGAGCCCG	0.711																																					p.L263L		Atlas-SNP	.											FAM131C,colon,carcinoma,0,1	FAM131C	21	1	0			c.C789A						PASS	.						2.0	2.0	2.0					1																	16384986		1272	2832	4104	SO:0001819	synonymous_variant	348487	exon7			GGAGGGGAGGGAG		CCDS41270.1	1p36.13	2008-02-05	2007-03-20	2007-03-20	ENSG00000185519	ENSG00000185519			26717	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 117"""	C1orf117		12477932	Standard	NM_182623		Approved	FLJ36766	uc001axz.4	Q96AQ9	OTTHUMG00000009525	ENST00000375662.4:c.789C>A	1.37:g.16384986G>T		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	124	5	0.0403226	NM_182623	Q5T5Q5|Q8N3X3|Q8N9P9	Silent	SNP	ENST00000375662.4	37	CCDS41270.1																																																																																			G|0.704;T|0.296	0.296	strong		0.711	FAM131C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026319.1	NM_182623	
SORCS1	114815	hgsc.bcm.edu	37	10	108380213	108380213	+	Silent	SNP	G	G	A	rs4917481	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr10:108380213G>A	ENST00000263054.6	-	20	2776	c.2769C>T	c.(2767-2769)taC>taT	p.Y923Y	SORCS1_ENST00000344440.6_Silent_p.Y923Y|SORCS1_ENST00000478809.2_5'Flank|SORCS1_ENST00000369698.1_Silent_p.Y458Y	NM_001206570.1|NM_052918.4	NP_001193499.1|NP_443150.3	Q8WY21	SORC1_HUMAN	sortilin-related VPS10 domain containing receptor 1	923					neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	neuropeptide receptor activity (GO:0008188)			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)		ACCACCACACGTAAGTGAGGG	0.547													A|||	1883	0.375998	0.4682	0.2435	5008	,	,		12097	0.5069		0.171	False		,,,				2504	0.4213				p.Y923Y		Atlas-SNP	.											.	SORCS1	534	.	0			c.C2769T						PASS	.	A	,,,,,	1883,2523	630.4+/-395.5	403,1077,723	170.0	136.0	147.0		2769,2769,2769,2769,2769,2769	-3.2	0.8	10	dbSNP_111	147	1450,7150	751.3+/-407.4	117,1216,2967	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SORCS1	NM_001013031.2,NM_001206569.1,NM_001206570.1,NM_001206571.1,NM_001206572.1,NM_052918.4	,,,,,	520,2293,3690	AA,AG,GG		16.8605,42.7372,25.6266	,,,,,	923/1199,923/1180,923/1131,923/1160,923/1180,923/1169	108380213	3333,9673	2203	4300	6503	SO:0001819	synonymous_variant	114815	exon20			CCACACGTAAGTG	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.2769C>T	10.37:g.108380213G>A		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	60	6	0.1	NM_001206572	A2RRF4|Q59GG7|Q5JVT7|Q5JVT8|Q5VY14|Q86WQ1|Q86WQ2|Q9H1Y1|Q9H1Y2	Silent	SNP	ENST00000263054.6	37	CCDS7559.1																																																																																			G|0.707;A|0.293	0.293	strong		0.547	SORCS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050232.4	NM_052918	
COL6A5	256076	hgsc.bcm.edu	37	3	130114190	130114190	+	Silent	SNP	C	C	T			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr3:130114190C>T	ENST00000432398.2	+	8	3944	c.3450C>T	c.(3448-3450)ctC>ctT	p.L1150L	COL6A5_ENST00000265379.6_Silent_p.L1150L	NM_153264.5	NP_694996.5	A8TX70	CO6A5_HUMAN	collagen, type VI, alpha 5	1150	Nonhelical region.|VWFA 6. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				endometrium(6)|kidney(4)|large_intestine(8)|lung(19)|pancreas(2)|prostate(3)|stomach(1)|urinary_tract(1)	44						AGGAACATCTCCTGCCAATAA	0.383																																					p.L1150L		Atlas-SNP	.											.	COL6A5	205	.	0			c.C3450T						PASS	.						17.0	16.0	16.0					3																	130114190		692	1591	2283	SO:0001819	synonymous_variant	256076	exon8			ACATCTCCTGCCA	AK093199		3q21.3	2013-01-16	2010-05-24	2010-05-24	ENSG00000172752	ENSG00000172752		"""Collagens"""	26674	protein-coding gene	gene with protein product	"""von Willebrand factor A domain containing 4"""	611916	"""collagen, type XXIX, alpha 1"""	COL29A1		17850181	Standard	NM_153264		Approved	FLJ35880, VWA4	uc010htk.2	A8TX70	OTTHUMG00000159712	ENST00000432398.2:c.3450C>T	3.37:g.130114190C>T		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	123	5	0.0406504	NM_153264	A9J6L2|A9J6L4|A9J6L6|A9J6L7|A9J6M0|A9J6M1|A9J6M2|B5MEA7|Q6ZW26|Q8NA36	Silent	SNP	ENST00000432398.2	37																																																																																				.	.	none		0.383	COL6A5-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_153264	
FAM131C	348487	hgsc.bcm.edu	37	1	16384998	16384998	+	Silent	SNP	G	G	C	rs1807285	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr1:16384998G>C	ENST00000375662.4	-	7	960	c.777C>G	c.(775-777)ccC>ccG	p.P259P	FAM131C_ENST00000494078.1_5'UTR	NM_182623.2	NP_872429.2	Q96AQ9	F131C_HUMAN	family with sequence similarity 131, member C	259	Pro-rich.									large_intestine(2)|lung(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	8		Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Colorectal(212;8.32e-08)|COAD - Colon adenocarcinoma(227;5.56e-06)|BRCA - Breast invasive adenocarcinoma(304;9.12e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.00656)|READ - Rectum adenocarcinoma(331;0.0649)		GGGAGCCCGGGGGGTGGGTCC	0.716													C|||	1887	0.376797	0.4032	0.2795	5008	,	,		19381	0.4315		0.336	False		,,,				2504	0.3957				p.P259P		Atlas-SNP	.											FAM131C,NS,carcinoma,-1,2	FAM131C	21	2	0			c.C777G						scavenged	.						2.0	2.0	2.0					1																	16384998		1394	3106	4500	SO:0001819	synonymous_variant	348487	exon7			GCCCGGGGGGTGG		CCDS41270.1	1p36.13	2008-02-05	2007-03-20	2007-03-20	ENSG00000185519	ENSG00000185519			26717	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 117"""	C1orf117		12477932	Standard	NM_182623		Approved	FLJ36766	uc001axz.4	Q96AQ9	OTTHUMG00000009525	ENST00000375662.4:c.777C>G	1.37:g.16384998G>C		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	129	5	0.0387597	NM_182623	Q5T5Q5|Q8N3X3|Q8N9P9	Silent	SNP	ENST00000375662.4	37	CCDS41270.1																																																																																			G|0.706;C|0.294	0.294	strong		0.716	FAM131C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026319.1	NM_182623	
ANKRD50	57182	hgsc.bcm.edu	37	4	125590478	125590478	+	Silent	SNP	T	T	C	rs1874748	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr4:125590478T>C	ENST00000504087.1	-	4	4991	c.3954A>G	c.(3952-3954)ccA>ccG	p.P1318P	ANKRD50_ENST00000515641.1_Silent_p.P1139P	NM_020337.2	NP_065070.1	Q9ULJ7	ANR50_HUMAN	ankyrin repeat domain 50	1318										NS(1)|breast(3)|central_nervous_system(1)|endometrium(7)|kidney(4)|large_intestine(14)|lung(18)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	55						TTTGTTTAGGTGGTGCAGCAG	0.398													T|||	1070	0.213658	0.2292	0.1816	5008	,	,		19308	0.2421		0.16	False		,,,				2504	0.2413				p.P1318P		Atlas-SNP	.											.	ANKRD50	136	.	0			c.A3954G						PASS	.	T	,	969,3437	363.1+/-316.4	99,771,1333	145.0	146.0	146.0		3417,3954	-10.4	0.0	4	dbSNP_92	146	1303,7297	257.5+/-281.5	107,1089,3104	no	coding-synonymous,coding-synonymous	ANKRD50	NM_001167882.1,NM_020337.2	,	206,1860,4437	CC,CT,TT		15.1512,21.9927,17.4689	,	1139/1251,1318/1430	125590478	2272,10734	2203	4300	6503	SO:0001819	synonymous_variant	57182	exon4			TTTAGGTGGTGCA	AB033049	CCDS34060.1, CCDS54802.1	4q28.1	2013-01-10			ENSG00000151458	ENSG00000151458		"""Ankyrin repeat domain containing"""	29223	protein-coding gene	gene with protein product							Standard	NM_020337		Approved	KIAA1223	uc010inw.3	Q9ULJ7	OTTHUMG00000161398	ENST00000504087.1:c.3954A>G	4.37:g.125590478T>C		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	132	7	0.0530303	NM_020337	A8K4V3|B4DHJ6|E9PDW0|Q6N064|Q6ZSE6	Silent	SNP	ENST00000504087.1	37	CCDS34060.1																																																																																			T|0.820;C|0.180	0.180	strong		0.398	ANKRD50-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364775.1	NM_020337	
TUBA3E	112714	hgsc.bcm.edu	37	2	130951949	130951949	+	Missense_Mutation	SNP	G	G	A	rs62165074	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr2:130951949G>A	ENST00000312988.7	-	4	566	c.466C>T	c.(466-468)Cgg>Tgg	p.R156W		NM_207312.2	NP_997195	Q6PEY2	TBA3E_HUMAN	tubulin, alpha 3e	156					microtubule-based process (GO:0007017)|protein polymerization (GO:0051258)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)			endometrium(4)|kidney(7)|large_intestine(6)|lung(9)|skin(2)	28	Colorectal(110;0.1)					ACTGAGAGCCGCTCCATGAGC	0.577																																					p.R156W		Atlas-SNP	.											TUBA3E,NS,carcinoma,+2,1	TUBA3E	73	1	0			c.C466T						scavenged	.	G	TRP/ARG	1567,2837	489.4+/-361.5	284,999,919	71.0	76.0	74.0		466	0.6	1.0	2	dbSNP_129	74	3350,5248	496.3+/-374.3	657,2036,1606	no	missense	TUBA3E	NM_207312.2	101	941,3035,2525	AA,AG,GG		38.9625,35.5813,37.8173	probably-damaging	156/451	130951949	4917,8085	2202	4299	6501	SO:0001583	missense	112714	exon4			AGAGCCGCTCCAT	BC057811	CCDS2158.1	2q21.1	2007-03-16			ENSG00000152086	ENSG00000152086		"""Tubulins"""	20765	protein-coding gene	gene with protein product							Standard	NM_207312		Approved		uc002tqv.3	Q6PEY2	OTTHUMG00000131626	ENST00000312988.7:c.466C>T	2.37:g.130951949G>A	ENSP00000318197:p.Arg156Trp	Somatic	335	0	0		WXS	Illumina HiSeq	Phase_I	327	12	0.0366972	NM_207312		Missense_Mutation	SNP	ENST00000312988.7	37	CCDS2158.1	874	0.4001831501831502	166	0.33739837398373984	163	0.45027624309392267	269	0.47027972027972026	276	0.3641160949868074	g	12.55	1.970279	0.34754	0.355813	0.389625	ENSG00000152086	ENST00000312988	T	0.71698	-0.59	2.71	0.549	0.17213	Tubulin/FtsZ, GTPase domain (4);	0.000000	0.49916	U	0.000125	T	0.00012	0.0000	H	0.98487	4.245	0.23700	P	0.99707653	D	0.71674	0.998	P	0.62649	0.905	T	0.18116	-1.0347	9	0.87932	D	0	.	4.7171	0.12899	0.1389:0.0:0.649:0.212	rs62165074	156	Q6PEY2	TBA3E_HUMAN	W	156	ENSP00000318197:R156W	ENSP00000318197:R156W	R	-	1	2	TUBA3E	130668419	1.000000	0.71417	1.000000	0.80357	0.938000	0.57974	1.313000	0.33585	0.485000	0.27652	0.449000	0.29647	CGG	G|0.500;A|0.500	0.500	weak		0.577	TUBA3E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254519.1	NM_207312	
SLC22A16	85413	hgsc.bcm.edu	37	6	110777962	110777962	+	Silent	SNP	A	A	G	rs6907567	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr6:110777962A>G	ENST00000368919.3	-	2	378	c.312T>C	c.(310-312)aaT>aaC	p.N104N	SLC22A16_ENST00000330550.4_Silent_p.N70N|SLC22A16_ENST00000456137.2_Silent_p.N104N|SLC22A16_ENST00000439654.1_Silent_p.N104N|SLC22A16_ENST00000461487.1_5'UTR	NM_033125.3	NP_149116.2	Q86VW1	S22AG_HUMAN	solute carrier family 22 (organic cation/carnitine transporter), member 16	104					acid secretion (GO:0046717)|amine transport (GO:0015837)|carnitine transmembrane transport (GO:1902603)|carnitine transport (GO:0015879)|cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|organic cation transport (GO:0015695)|single fertilization (GO:0007338)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	amine transmembrane transporter activity (GO:0005275)|carnitine transmembrane transporter activity (GO:0015226)|organic cation transmembrane transporter activity (GO:0015101)			breast(1)|endometrium(1)|kidney(3)|large_intestine(6)|lung(16)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	34		all_cancers(87;0.00221)|Acute lymphoblastic leukemia(125;2.27e-07)|all_hematologic(75;1.38e-05)|all_epithelial(87;0.0485)|Colorectal(196;0.101)		OV - Ovarian serous cystadenocarcinoma(136;0.0513)|Epithelial(106;0.0921)|all cancers(137;0.115)	Doxorubicin(DB00997)|L-Carnitine(DB00583)	TCTCCCTCTTATTCCTGCTAC	0.473													G|||	1573	0.314097	0.3888	0.2406	5008	,	,		19928	0.4107		0.2207	False		,,,				2504	0.2618				p.N104N		Atlas-SNP	.											.	SLC22A16	81	.	0			c.T312C						PASS	.	G		1600,2806	663.6+/-401.2	281,1038,884	241.0	238.0	239.0		312	0.3	0.0	6	dbSNP_116	239	1917,6683	726.4+/-406.6	180,1557,2563	no	coding-synonymous	SLC22A16	NM_033125.2		461,2595,3447	GG,GA,AA		22.2907,36.3141,27.0414		104/578	110777962	3517,9489	2203	4300	6503	SO:0001819	synonymous_variant	85413	exon2			CCTCTTATTCCTG		CCDS5084.1	6q21	2013-05-22	2008-01-11		ENSG00000004809	ENSG00000004809		"""Solute carriers"""	20302	protein-coding gene	gene with protein product		608276	"""solute carrier family 22 (organic cation transporter), member 16"""			12372408, 12089149, 17473959	Standard	NM_033125		Approved	FLIPT2, CT2, OKB1, OAT6	uc003puf.3	Q86VW1	OTTHUMG00000016171	ENST00000368919.3:c.312T>C	6.37:g.110777962A>G		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	70	4	0.0571429	NM_033125	O14567|Q5JXM1|Q8IUG8|Q8IZD5|Q96M90|Q96RU0	Silent	SNP	ENST00000368919.3	37	CCDS5084.1																																																																																			A|0.716;G|0.284	0.284	strong		0.473	SLC22A16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043428.1	NM_033125	
CMYA5	202333	hgsc.bcm.edu	37	5	79029749	79029749	+	Missense_Mutation	SNP	A	A	G	rs1428225	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr5:79029749A>G	ENST00000446378.2	+	2	5192	c.5161A>G	c.(5161-5163)Atc>Gtc	p.I1721V		NM_153610.3	NP_705838.3	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	1721			I -> V (in dbSNP:rs1428225).		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)		p.I1721V(1)		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)		TCCCAAGATCATCAGCCTAGA	0.418													G|||	1389	0.277356	0.5961	0.085	5008	,	,		18104	0.3621		0.0815	False		,,,				2504	0.0971				p.I1721V		Atlas-SNP	.											CMYA5,NS,carcinoma,0,1	CMYA5	643	1	1	Substitution - Missense(1)	stomach(1)	c.A5161G						PASS	.	G	VAL/ILE	1877,1849		487,903,473	50.0	52.0	52.0		5161	2.8	0.0	5	dbSNP_88	52	707,7475		39,629,3423	yes	missense	CMYA5	NM_153610.3	29	526,1532,3896	GG,GA,AA		8.6409,49.6243,21.6997	benign	1721/4070	79029749	2584,9324	1863	4091	5954	SO:0001583	missense	202333	exon2			AAGATCATCAGCC	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.5161A>G	5.37:g.79029749A>G	ENSP00000394770:p.Ile1721Val	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	104	10	0.0961538	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	627	0.28708791208791207	305	0.6199186991869918	31	0.0856353591160221	232	0.40559440559440557	59	0.07783641160949868	G	0.001	-3.170670	0.00027	0.503757	0.086409	ENSG00000164309	ENST00000446378	T	0.37752	1.18	3.64	2.77	0.32553	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.47086	-0.9144	8	0.02654	T	1	.	4.7036	0.12839	0.1166:0.0:0.6708:0.2126	rs1428225;rs16877145;rs57809833	1721	Q8N3K9	CMYA5_HUMAN	V	1721	ENSP00000394770:I1721V	ENSP00000394770:I1721V	I	+	1	0	CMYA5	79065505	0.005000	0.15991	0.009000	0.14445	0.001000	0.01503	0.467000	0.22035	0.110000	0.17919	-0.913000	0.02753	ATC	A|0.752;G|0.248	0.248	strong		0.418	CMYA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369497.1	NM_153610	
RCAN3	11123	hgsc.bcm.edu	37	1	24861704	24861704	+	Silent	SNP	G	G	A	rs196432	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr1:24861704G>A	ENST00000374395.4	+	5	976	c.663G>A	c.(661-663)acG>acA	p.T221T	RCAN3_ENST00000436717.2_Silent_p.T211T|RCAN3_ENST00000538532.1_Silent_p.T163T|RCAN3_ENST00000374393.2_Missense_Mutation_p.R106Q|RCAN3_ENST00000412742.2_Missense_Mutation_p.R164Q	NM_001251978.1|NM_001251979.1|NM_001251984.1	NP_001238907.1|NP_001238908.1|NP_001238913.1	Q9UKA8	RCAN3_HUMAN	RCAN family member 3	221					anatomical structure morphogenesis (GO:0009653)|calcium-mediated signaling (GO:0019722)		RNA binding (GO:0003723)|troponin I binding (GO:0031013)			central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(2)	7		Colorectal(325;3.46e-05)|Renal(390;0.0007)|Lung NSC(340;0.000946)|all_lung(284;0.00125)|Ovarian(437;0.00473)|Breast(348;0.0148)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.19)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0427)|OV - Ovarian serous cystadenocarcinoma(117;1.13e-24)|Colorectal(126;6.09e-08)|COAD - Colon adenocarcinoma(152;3.33e-06)|GBM - Glioblastoma multiforme(114;0.000923)|BRCA - Breast invasive adenocarcinoma(304;0.0018)|KIRC - Kidney renal clear cell carcinoma(1967;0.00359)|STAD - Stomach adenocarcinoma(196;0.00493)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.14)		TTGCCCAGACGAGGCGCCCCG	0.582													G|||	2550	0.509185	0.4667	0.4006	5008	,	,		15419	0.7272		0.4573	False		,,,				2504	0.4724				p.R164Q		Atlas-SNP	.											RCAN3,colon,carcinoma,0,1	RCAN3	22	1	0			c.G491A						scavenged	.	G		2045,2361	566.1+/-381.8	472,1101,630	53.0	55.0	54.0		663	-11.6	0.0	1	dbSNP_79	54	3966,4634	548.7+/-385.4	893,2180,1227	no	coding-synonymous	RCAN3	NM_013441.2		1365,3281,1857	AA,AG,GG		46.1163,46.414,46.2171		221/242	24861704	6011,6995	2203	4300	6503	SO:0001819	synonymous_variant	11123	exon3			CCAGACGAGGCGC		CCDS254.1, CCDS57980.1, CCDS57981.1, CCDS57982.1, CCDS72730.1	1p35.3-p33	2008-02-05	2007-06-26	2007-06-26	ENSG00000117602	ENSG00000117602			3042	protein-coding gene	gene with protein product		605860	"""Down syndrome critical region gene 1-like 2"""	DSCR1L2		10756093	Standard	NM_001251984		Approved		uc001bjj.3	Q9UKA8	OTTHUMG00000003298	ENST00000374395.4:c.663G>A	1.37:g.24861704G>A		Somatic	130	2	0.0153846		WXS	Illumina HiSeq	Phase_I	154	5	0.0324675	NM_001251982	A4GU14|A4LA69|E3VWE2|E5L4P0|E5L4P7|E7ENV1|E7EWD8|G1FI66|G1FLF0|Q5ECL3|Q5TGC6|Q9NUC8|Q9UKA7	Missense_Mutation	SNP	ENST00000374395.4	37	CCDS254.1	1141	0.5224358974358975	218	0.44308943089430897	141	0.38950276243093923	416	0.7272727272727273	366	0.48284960422163586	G	0.029	-1.348475	0.01266	0.46414	0.461163	ENSG00000117602	ENST00000412742;ENST00000374393	.	.	.	5.78	-11.6	0.00059	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.58432	P	1.0000000000287557E-6	B;B	0.15719	0.014;0.0	B;B	0.10450	0.005;0.0	T	0.19844	-1.0293	6	0.06757	T	0.87	-5.9522	9.401	0.38433	0.4826:0.3354:0.1284:0.0537	rs196432;rs548092;rs3765891;rs17441326;rs17846158;rs17859166;rs60263682;rs196432	106;164	E7EWD8;E7ENV1	.;.	Q	164;106	.	ENSP00000363514:R106Q	R	+	2	0	RCAN3	24734291	0.000000	0.05858	0.000000	0.03702	0.036000	0.12997	-3.588000	0.00422	-4.477000	0.00046	-1.753000	0.00675	CGA	G|0.515;A|0.485	0.485	strong		0.582	RCAN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009176.2		
DMXL2	23312	hgsc.bcm.edu	37	15	51795172	51795172	+	Silent	SNP	G	G	A	rs12592889	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr15:51795172G>A	ENST00000251076.5	-	17	3110	c.2823C>T	c.(2821-2823)aaC>aaT	p.N941N	DMXL2_ENST00000449909.3_Intron|DMXL2_ENST00000543779.2_Silent_p.N941N	NM_001174116.1|NM_015263.3	NP_001167587.1|NP_056078.2	Q8TDJ6	DMXL2_HUMAN	Dmx-like 2	941						cell junction (GO:0030054)|extracellular space (GO:0005615)|membrane (GO:0016020)|synaptic vesicle (GO:0008021)	Rab GTPase binding (GO:0017137)	p.N941N(1)		breast(4)|central_nervous_system(1)|cervix(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(26)|liver(1)|lung(28)|ovary(7)|prostate(7)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	101				all cancers(107;0.00494)		AAGAATCTACGTTCTTCTGTC	0.378													A|||	2060	0.411342	0.3011	0.4813	5008	,	,		16613	0.4077		0.5159	False		,,,				2504	0.407				p.N941N		Atlas-SNP	.											DMXL2,NS,carcinoma,0,1	DMXL2	262	1	1	Substitution - coding silent(1)	stomach(1)	c.C2823T						scavenged	.	A	,,	1548,2842	669.4+/-402.2	277,994,924	89.0	93.0	92.0		2823,,2823	-0.2	0.0	15	dbSNP_120	92	4328,4258	573.8+/-389.9	1103,2122,1068	no	coding-synonymous,intron,coding-synonymous	DMXL2	NM_001174116.1,NM_001174117.1,NM_015263.3	,,	1380,3116,1992	AA,AG,GG		49.5924,35.262,45.2836	,,	941/3038,,941/3037	51795172	5876,7100	2195	4293	6488	SO:0001819	synonymous_variant	23312	exon17			ATCTACGTTCTTC	AB020663	CCDS10141.1, CCDS53945.1, CCDS53946.1	15q21.2	2013-01-10			ENSG00000104093	ENSG00000104093		"""WD repeat domain containing"""	2938	protein-coding gene	gene with protein product	"""rabconnectin 3"""	612186					Standard	NM_001174116		Approved	RC3, KIAA0856	uc010ufy.2	Q8TDJ6	OTTHUMG00000131749	ENST00000251076.5:c.2823C>T	15.37:g.51795172G>A		Somatic	170	1	0.00588235		WXS	Illumina HiSeq	Phase_I	198	10	0.050505	NM_001174116	B2RTR3|B7ZMH3|F5GWF1|O94938	Silent	SNP	ENST00000251076.5	37	CCDS10141.1																																																																																			G|0.548;A|0.452	0.452	strong		0.378	DMXL2-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254671.2	NM_015263	
PTPRS	5802	hgsc.bcm.edu	37	19	5222916	5222916	+	Missense_Mutation	SNP	C	C	T	rs62113240		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr19:5222916C>T	ENST00000587303.1	-	17	2986	c.2887G>A	c.(2887-2889)Gtc>Atc	p.V963I	PTPRS_ENST00000348075.2_Missense_Mutation_p.V941I|PTPRS_ENST00000353284.2_Intron|PTPRS_ENST00000357368.4_Missense_Mutation_p.V963I|PTPRS_ENST00000588552.1_Intron|PTPRS_ENST00000262963.6_Missense_Mutation_p.V959I|PTPRS_ENST00000372412.4_Missense_Mutation_p.V964I|PTPRS_ENST00000592099.1_Intron|PTPRS_ENST00000588012.1_Missense_Mutation_p.V941I			Q13332	PTPRS_HUMAN	protein tyrosine phosphatase, receptor type, S	963	Fibronectin type-III 7. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|corpus callosum development (GO:0022038)|extracellular matrix organization (GO:0030198)|hippocampus development (GO:0021766)|peptidyl-tyrosine dephosphorylation (GO:0035335)|spinal cord development (GO:0021510)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|biliary_tract(1)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|liver(1)|lung(9)|ovary(4)|prostate(1)|skin(12)|stomach(2)|upper_aerodigestive_tract(1)	61				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0321)|Lung(535;0.182)	Alendronate(DB00630)|Etidronic acid(DB01077)	GTGTATTTGACGATGGCCCCG	0.741																																					p.V963I		Atlas-SNP	.											.	PTPRS	169	.	0			c.G2887A						PASS	.						4.0	6.0	6.0					19																	5222916		1894	3710	5604	SO:0001583	missense	5802	exon18			ATTTGACGATGGC	U35234	CCDS12139.1, CCDS12140.1, CCDS45930.1, CCDS74265.1	19p13.3	2013-02-11				ENSG00000105426		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	9681	protein-coding gene	gene with protein product		601576				8954782, 8524829	Standard	NM_002850		Approved		uc002mbv.3	Q13332		ENST00000587303.1:c.2887G>A	19.37:g.5222916C>T	ENSP00000467537:p.Val963Ile	Somatic	8	0	0		WXS	Illumina HiSeq	Phase_I	19	9	0.473684	NM_002850	O75255|O75870|Q15718|Q16341|Q2M3R7	Missense_Mutation	SNP	ENST00000587303.1	37	CCDS45930.1	.	.	.	.	.	.	.	.	.	.	C	9.675	1.147719	0.21288	.	.	ENSG00000105426	ENST00000372412;ENST00000357368;ENST00000355005;ENST00000356037;ENST00000262963;ENST00000348075	T;T;T;T	0.57752	0.38;0.38;0.38;0.38	4.01	0.642	0.17765	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.320832	0.23319	N	0.049473	T	0.26484	0.0647	N	0.11789	0.175	0.80722	D	1	B;B	0.12630	0.001;0.006	B;B	0.11329	0.002;0.006	T	0.06127	-1.0844	10	0.11794	T	0.64	.	7.107	0.25368	0.0:0.6232:0.0:0.3768	rs62113240	941;963	Q13332-6;Q13332	.;PTPRS_HUMAN	I	964;963;963;954;959;941	ENSP00000361489:V964I;ENSP00000349932:V963I;ENSP00000262963:V959I;ENSP00000269907:V941I	ENSP00000262963:V959I	V	-	1	0	PTPRS	5173916	0.966000	0.33281	0.984000	0.44739	0.983000	0.72400	0.897000	0.28390	0.039000	0.15632	0.557000	0.71058	GTC	.	.	weak		0.741	PTPRS-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000450762.2		
UBR4	23352	hgsc.bcm.edu	37	1	19447843	19447843	+	Silent	SNP	C	C	G	rs1044010	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr1:19447843C>G	ENST00000375254.3	-	68	10008	c.9981G>C	c.(9979-9981)ctG>ctC	p.L3327L	UBR4_ENST00000375267.2_Silent_p.L3327L|UBR4_ENST00000375226.2_Silent_p.L3303L|UBR4_ENST00000375217.2_Silent_p.L3320L|UBR4_ENST00000375218.3_5'Flank	NM_020765.2	NP_065816.2	Q5T4S7	UBR4_HUMAN	ubiquitin protein ligase E3 component n-recognin 4	3327					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)		TGCTGCCGCACAGAGCACAGG	0.602													C|||	3007	0.600439	0.5424	0.6844	5008	,	,		8659	0.7589		0.5775	False		,,,				2504	0.4796				p.L3327L		Atlas-SNP	.											UBR4,colon,carcinoma,0,1	UBR4	415	1	0			c.G9981C						scavenged	.	C		2419,1987	616.9+/-392.9	670,1079,454	66.0	64.0	65.0		9981	1.8	1.0	1	dbSNP_86	65	4866,3734	618.0+/-396.7	1392,2082,826	no	coding-synonymous	UBR4	NM_020765.2		2062,3161,1280	GG,GC,CC		43.4186,45.0976,43.9874		3327/5184	19447843	7285,5721	2203	4300	6503	SO:0001819	synonymous_variant	23352	exon68			GCCGCACAGAGCA	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.9981G>C	1.37:g.19447843C>G		Somatic	307	2	0.00651466		WXS	Illumina HiSeq	Phase_I	317	12	0.0378549	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																																																																																			C|0.417;G|0.583	0.583	strong		0.602	UBR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007085.1	NM_020765	
C16orf62	57020	hgsc.bcm.edu	37	16	19680546	19680546	+	Silent	SNP	T	T	C	rs957676	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr16:19680546T>C	ENST00000251143.5	+	27	2298	c.2286T>C	c.(2284-2286)gaT>gaC	p.D762D	C16orf62_ENST00000448695.1_Silent_p.D612D|C16orf62_ENST00000542263.1_Silent_p.D758D|C16orf62_ENST00000438132.3_Silent_p.D851D|C16orf62_ENST00000417362.2_Silent_p.D669D|C16orf62_ENST00000543152.1_Silent_p.D511D			Q7Z3J2	CP062_HUMAN	chromosome 16 open reading frame 62	762						integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(3)|kidney(5)|large_intestine(7)|liver(1)|lung(11)|ovary(1)|prostate(2)|skin(1)|urinary_tract(2)	36						TTAATATTGATGGGAAGATGC	0.408													C|||	1627	0.32488	0.3729	0.3098	5008	,	,		19645	0.2887		0.34	False		,,,				2504	0.2924				p.D851D		Atlas-SNP	.											.	C16orf62	164	.	0			c.T2553C						PASS	.	C		1628,2764	659.7+/-400.6	290,1048,858	118.0	117.0	118.0		2553	-2.5	0.6	16	dbSNP_86	118	2851,5749	674.3+/-403.1	467,1917,1916	no	coding-synonymous	C16orf62	NM_020314.5		757,2965,2774	CC,CT,TT		33.1512,37.0674,34.4751		851/1053	19680546	4479,8513	2196	4300	6496	SO:0001819	synonymous_variant	57020	exon27			TATTGATGGGAAG		CCDS32397.1, CCDS32397.2, CCDS73840.1	16p12.3	2012-05-30			ENSG00000103544	ENSG00000103544			24641	protein-coding gene	gene with protein product						10493829	Standard	NM_020314		Approved	MGC16824	uc002dgn.3	Q7Z3J2	OTTHUMG00000167925	ENST00000251143.5:c.2286T>C	16.37:g.19680546T>C		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	76	5	0.0657895	NM_020314	A8K2M1|O43329|Q69YI1|Q6PDA0|Q7L371|Q86W66|Q8WXA5|Q9H0L7|Q9H7C8	Silent	SNP	ENST00000251143.5	37																																																																																				T|0.656;C|0.344	0.344	strong		0.408	C16orf62-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_020314	
MYO3A	53904	hgsc.bcm.edu	37	10	26462790	26462790	+	Silent	SNP	G	G	A	rs3740232	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr10:26462790G>A	ENST00000265944.5	+	30	3763	c.3597G>A	c.(3595-3597)gaG>gaA	p.E1199E	MYO3A_ENST00000543632.1_Intron	NM_017433.4	NP_059129.3	Q8NEV4	MYO3A_HUMAN	myosin IIIA	1199					ATP catabolic process (GO:0006200)|inner ear development (GO:0048839)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of filopodium assembly (GO:0051491)|protein autophosphorylation (GO:0046777)|response to stimulus (GO:0050896)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|filopodium (GO:0030175)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|photoreceptor inner segment (GO:0001917)|stereocilium bundle tip (GO:0032426)	actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|plus-end directed microfilament motor activity (GO:0060002)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.E1199E(1)		NS(2)|breast(9)|central_nervous_system(3)|endometrium(9)|kidney(10)|large_intestine(28)|liver(1)|lung(46)|ovary(11)|pancreas(1)|prostate(6)|skin(11)|stomach(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	146						ATGAGGAAGAGGTTAAGCAAG	0.418													G|||	1648	0.329073	0.2262	0.317	5008	,	,		19882	0.3532		0.3429	False		,,,				2504	0.4376				p.E1199E		Atlas-SNP	.											MYO3A,colon,carcinoma,0,2	MYO3A	371	2	1	Substitution - coding silent(1)	stomach(1)	c.G3597A						scavenged	.	G		1105,3301	396.7+/-330.2	139,827,1237	87.0	86.0	86.0		3597	0.0	0.0	10	dbSNP_107	86	2884,5716	452.0+/-362.8	486,1912,1902	no	coding-synonymous	MYO3A	NM_017433.4		625,2739,3139	AA,AG,GG		33.5349,25.0794,30.6705		1199/1617	26462790	3989,9017	2203	4300	6503	SO:0001819	synonymous_variant	53904	exon30			GGAAGAGGTTAAG	AF229172	CCDS7148.1	10p11.1	2011-09-27	2004-05-19		ENSG00000095777	ENSG00000095777		"""Myosins / Myosin superfamily : Class III"""	7601	protein-coding gene	gene with protein product		606808	"""deafness, autosomal recessive 30"""	DFNB30		10936054	Standard	NM_017433		Approved		uc001isn.2	Q8NEV4	OTTHUMG00000017837	ENST00000265944.5:c.3597G>A	10.37:g.26462790G>A		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	162	2	0.0123457	NM_017433	Q4G0X2|Q5VZ28|Q8WX17|Q9NYS8	Silent	SNP	ENST00000265944.5	37	CCDS7148.1																																																																																			G|0.681;A|0.319	0.319	strong		0.418	MYO3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047259.1	NM_017433	
CCDC86	79080	hgsc.bcm.edu	37	11	60610065	60610065	+	Silent	SNP	G	G	A	rs141728952|rs2074420	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr11:60610065G>A	ENST00000227520.5	+	1	522	c.468G>A	c.(466-468)ccG>ccA	p.P156P	RP11-804A23.2_ENST00000539897.1_RNA|RP11-804A23.4_ENST00000538705.1_RNA	NM_024098.3	NP_077003.1	Q9H6F5	CCD86_HUMAN	coiled-coil domain containing 86	156	Pro-rich.				viral process (GO:0016032)	nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(1)|large_intestine(2)|liver(2)|lung(2)|urinary_tract(3)	10						AGCTACCGCCGGTCCCAGGAT	0.662													G|||	1707	0.340855	0.1664	0.2752	5008	,	,		14318	0.6806		0.1899	False		,,,				2504	0.4284				p.P156P		Atlas-SNP	.											CCDC86,NS,carcinoma,0,1	CCDC86	24	1	0			c.G468A						PASS	.						25.0	31.0	29.0					11																	60610065		2196	4289	6485	SO:0001819	synonymous_variant	79080	exon1			ACCGCCGGTCCCA	AK025974	CCDS7993.1	11q12.2	2006-03-16			ENSG00000110104	ENSG00000110104			28359	protein-coding gene	gene with protein product		611293					Standard	NM_024098		Approved	MGC2574	uc001nqa.2	Q9H6F5	OTTHUMG00000167706	ENST00000227520.5:c.468G>A	11.37:g.60610065G>A		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	104	5	0.0480769	NM_024098	B4DY99	Silent	SNP	ENST00000227520.5	37	CCDS7993.1																																																																																			G|0.725;A|0.275	0.275	strong		0.662	CCDC86-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395743.1	NM_024098	
DNAJC25	548645	hgsc.bcm.edu	37	9	114411945	114411945	+	Silent	SNP	G	G	T	rs7019332	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr9:114411945G>T	ENST00000313525.3	+	3	758	c.702G>T	c.(700-702)ggG>ggT	p.G234G	DNAJC25_ENST00000556107.1_Intron|DNAJC25-GNG10_ENST00000374294.3_Intron	NM_001015882.2	NP_001015882.2	Q9H1X3	DJC25_HUMAN	DnaJ (Hsp40) homolog, subfamily C , member 25	234						integral component of membrane (GO:0016021)				kidney(1)|large_intestine(2)|lung(1)|skin(4)	8						ATATAAAGGGGGGCTATCAGA	0.353													G|||	1563	0.312101	0.3517	0.4251	5008	,	,		18464	0.4127		0.2306	False		,,,				2504	0.1585				p.G234G		Atlas-SNP	.											.	DNAJC25	20	.	0			c.G702T						PASS	.	G	,	1147,2465		194,759,853	41.0	42.0	42.0		702,	-0.3	1.0	9	dbSNP_116	42	1718,6410		175,1368,2521	no	coding-synonymous,intron	DNAJC25,DNAJC25-GNG10	NM_001015882.2,NM_004125.3	,	369,2127,3374	TT,TG,GG		21.1368,31.7553,24.4037	,	234/361,	114411945	2865,8875	1806	4064	5870	SO:0001819	synonymous_variant	548645	exon3			AAAGGGGGGCTAT		CCDS43862.1	9q31.3	2011-09-02			ENSG00000059769	ENSG00000059769		"""Heat shock proteins / DNAJ (HSP40)"""	34187	protein-coding gene	gene with protein product							Standard	NM_001015882		Approved	bA16L21.2.1	uc004bfl.3	Q9H1X3	OTTHUMG00000020491	ENST00000313525.3:c.702G>T	9.37:g.114411945G>T		Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	210	9	0.0428571	NM_001015882	Q5QTD8|Q96BN9	Silent	SNP	ENST00000313525.3	37	CCDS43862.1																																																																																			G|0.691;T|0.309	0.309	strong		0.353	DNAJC25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000156218.3	NM_001015882	
JAG2	3714	hgsc.bcm.edu	37	14	105615648	105615648	+	Missense_Mutation	SNP	C	C	T	rs9972231	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr14:105615648C>T	ENST00000331782.3	-	13	2015	c.1612G>A	c.(1612-1614)Gac>Aac	p.D538N	JAG2_ENST00000347004.2_Missense_Mutation_p.D500N|RP11-44N21.4_ENST00000548203.1_RNA	NM_002226.4	NP_002217.3	Q9Y219	JAG2_HUMAN	jagged 2	538	EGF-like 9. {ECO:0000255|PROSITE- ProRule:PRU00076}.		D -> N (in dbSNP:rs9972231).		auditory receptor cell fate commitment (GO:0009912)|cell cycle (GO:0007049)|cell differentiation (GO:0030154)|epithelial cell apoptotic process involved in palatal shelf morphogenesis (GO:1990134)|gamma-delta T cell differentiation (GO:0042492)|in utero embryonic development (GO:0001701)|morphogenesis of embryonic epithelium (GO:0016331)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|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)|respiratory system process (GO:0003016)|skeletal system development (GO:0001501)|spermatogenesis (GO:0007283)|T cell differentiation (GO:0030217)|thymic T cell selection (GO:0045061)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|growth factor activity (GO:0008083)|Notch binding (GO:0005112)	p.D538N(2)		breast(2)|endometrium(2)|kidney(3)|large_intestine(1)|lung(7)|prostate(2)|skin(5)	22		all_cancers(154;0.0336)|all_epithelial(191;0.0729)|Melanoma(154;0.155)	OV - Ovarian serous cystadenocarcinoma(23;0.00989)|all cancers(16;0.0114)|Epithelial(46;0.0272)	Epithelial(152;0.047)|OV - Ovarian serous cystadenocarcinoma(161;0.148)|all cancers(159;0.208)		TCACAAAGGTCGACATCCACC	0.622													c|||	601	0.120008	0.0053	0.1268	5008	,	,		11943	0.1687		0.1312	False		,,,				2504	0.2086				p.D538N		Atlas-SNP	.											JAG2,scalp,carcinoma,0,3	JAG2	69	3	2	Substitution - Missense(2)	lung(1)|skin(1)	c.G1612A						scavenged	.		ASN/ASP,ASN/ASP	143,4261	98.9+/-137.6	2,139,2061	68.0	71.0	70.0		1612,1498	3.8	0.0	14	dbSNP_119	70	1119,7481	229.8+/-264.4	82,955,3263	yes	missense,missense	JAG2	NM_002226.3,NM_145159.1	23,23	84,1094,5324	TT,TC,CC		13.0116,3.247,9.7047	possibly-damaging,possibly-damaging	538/1239,500/1201	105615648	1262,11742	2202	4300	6502	SO:0001583	missense	3714	exon13			AAAGGTCGACATC	AF020201	CCDS9998.1, CCDS9999.1	14q32	2008-08-01			ENSG00000184916	ENSG00000184916			6189	protein-coding gene	gene with protein product		602570				9315665, 10662552	Standard	NM_002226		Approved		uc001yqg.4	Q9Y219	OTTHUMG00000140172	ENST00000331782.3:c.1612G>A	14.37:g.105615648C>T	ENSP00000328169:p.Asp538Asn	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	97	3	0.0309278	NM_002226	Q9UE17|Q9UE99|Q9UNK8|Q9Y6P9|Q9Y6Q0	Missense_Mutation	SNP	ENST00000331782.3	37	CCDS9998.1	253	0.11584249084249085	5	0.01016260162601626	44	0.12154696132596685	104	0.18181818181818182	100	0.13192612137203166	C	12.41	1.928193	0.34002	0.03247	0.130116	ENSG00000184916	ENST00000331782;ENST00000347004	D;D	0.83673	-1.75;-1.75	3.8	3.8	0.43715	EGF-like calcium-binding (1);Epidermal growth factor-like, type 3 (1);	0.056989	0.64402	D	0.000002	T	0.00412	0.0013	L	0.49455	1.56	0.21020	P	0.999805715	B;B	0.34147	0.438;0.202	B;B	0.29267	0.1;0.025	T	0.30238	-0.9985	9	0.20519	T	0.43	.	13.511	0.61513	0.0:1.0:0.0:0.0	rs9972231;rs57317492;rs9972231	500;538	Q9Y219-2;Q9Y219	.;JAG2_HUMAN	N	538;500	ENSP00000328169:D538N;ENSP00000328566:D500N	ENSP00000328169:D538N	D	-	1	0	JAG2	104686693	0.269000	0.24143	0.038000	0.18304	0.038000	0.13279	0.959000	0.29240	1.830000	0.53286	0.556000	0.70494	GAC	C|0.899;T|0.101	0.101	strong		0.622	JAG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276506.2		
BST1	683	hgsc.bcm.edu	37	4	15733454	15733454	+	Silent	SNP	A	A	C	rs1058212	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr4:15733454A>C	ENST00000265016.4	+	9	1138	c.943A>C	c.(943-945)Agg>Cgg	p.R315R	BST1_ENST00000382346.3_Silent_p.R330R	NM_004334.2	NP_004325.2	Q10588	BST1_HUMAN	bone marrow stromal cell antigen 1	315					humoral immune response (GO:0006959)|multicellular organismal development (GO:0007275)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|plasma membrane (GO:0005886)	NAD(P)+ nucleosidase activity (GO:0050135)|NAD+ nucleosidase activity (GO:0003953)|transferase activity (GO:0016740)	p.R315R(2)		central_nervous_system(1)|large_intestine(1)|lung(2)|stomach(3)|urinary_tract(1)	8						GCTGGCTTCCAGGACTCAACT	0.493													G|||	931	0.185903	0.115	0.0951	5008	,	,		16685	0.502		0.0308	False		,,,				2504	0.18				p.R315R		Atlas-SNP	.											BST1,colon,carcinoma,0,3	BST1	30	3	2	Substitution - coding silent(2)	stomach(1)|central_nervous_system(1)	c.A943C						scavenged	.	G		506,3900		26,454,1723	55.0	52.0	53.0		943	4.0	0.0	4	dbSNP_86	53	260,8340		3,254,4043	no	coding-synonymous	BST1	NM_004334.2		29,708,5766	CC,CA,AA		3.0233,11.4843,5.8896		315/319	15733454	766,12240	2203	4300	6503	SO:0001819	synonymous_variant	683	exon9			GCTTCCAGGACTC	D21878	CCDS3416.1	4p15	2010-05-04			ENSG00000109743	ENSG00000109743	3.2.2.5	"""CD molecules"""	1118	protein-coding gene	gene with protein product	"""NAD(+) nucleosidase"", ""ADP-ribosyl cyclase 2"""	600387				8202488	Standard	NM_004334		Approved	CD157	uc003goh.4	Q10588	OTTHUMG00000097739	ENST00000265016.4:c.943A>C	4.37:g.15733454A>C		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	160	4	0.025	NM_004334	B2R6A2|Q1XII0|Q5U0K0|Q96EN3	Silent	SNP	ENST00000265016.4	37	CCDS3416.1																																																																																			A|0.883;C|0.117	0.117	strong		0.493	BST1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000214968.2	NM_004334	
ELL2	22936	hgsc.bcm.edu	37	5	95236415	95236415	+	Silent	SNP	G	G	A	rs17085249	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr5:95236415G>A	ENST00000237853.4	-	7	1285	c.936C>T	c.(934-936)gaC>gaT	p.D312D	ELL2_ENST00000431061.2_Intron	NM_012081.5	NP_036213.2	O00472	ELL2_HUMAN	elongation factor, RNA polymerase II, 2	312					regulation of transcription, DNA-templated (GO:0006355)|snRNA transcription from RNA polymerase II promoter (GO:0042795)|transcription elongation from RNA polymerase II promoter (GO:0006368)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)		p.D312D(1)		breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(10)|pancreas(1)|prostate(2)	24		all_cancers(142;2.04e-06)|all_epithelial(76;3.1e-09)|all_lung(232;0.00309)|Lung NSC(167;0.00454)|Ovarian(225;0.0165)|Colorectal(57;0.0343)|Breast(839;0.198)		all cancers(79;2.16e-15)		AAGATACAGCGTCTCTACTAG	0.413													G|||	1706	0.340655	0.3654	0.2406	5008	,	,		19046	0.4325		0.2793	False		,,,				2504	0.3466				p.D312D		Atlas-SNP	.											ELL2,NS,carcinoma,0,1	ELL2	63	1	1	Substitution - coding silent(1)	prostate(1)	c.C936T						scavenged	.	G		1503,2903	478.5+/-358.2	256,991,956	75.0	73.0	73.0		936	-8.4	0.0	5	dbSNP_123	73	2247,6353	380.4+/-339.6	290,1667,2343	no	coding-synonymous	ELL2	NM_012081.5		546,2658,3299	AA,AG,GG		26.1279,34.1126,28.8328		312/641	95236415	3750,9256	2203	4300	6503	SO:0001819	synonymous_variant	22936	exon7			TACAGCGTCTCTA	U88629	CCDS4080.1	5q15	2010-11-29			ENSG00000118985	ENSG00000118985			17064	protein-coding gene	gene with protein product		601874				9108030	Standard	NM_012081		Approved		uc003klr.4	O00472	OTTHUMG00000122085	ENST00000237853.4:c.936C>T	5.37:g.95236415G>A		Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	179	6	0.0335196	NM_012081	B4DNK7	Silent	SNP	ENST00000237853.4	37	CCDS4080.1																																																																																			G|0.697;A|0.303	0.303	strong		0.413	ELL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242846.1	NM_012081	
LILRA4	23547	hgsc.bcm.edu	37	19	54848741	54848741	+	Silent	SNP	T	T	C	rs12985462	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr19:54848741T>C	ENST00000291759.4	-	5	938	c.882A>G	c.(880-882)agA>agG	p.R294R	AC008984.2_ENST00000507363.1_RNA	NM_012276.3	NP_036408.3	P59901	LIRA4_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 4	294	Ig-like C2-type 3.				immune system process (GO:0002376)	integral component of membrane (GO:0016021)				NS(2)|breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(5)|lung(13)|prostate(3)|skin(1)|upper_aerodigestive_tract(3)	32	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.0565)		CGCCGTAGCATCTGTACTGGC	0.692													T|||	872	0.174121	0.0204	0.2262	5008	,	,		13206	0.2143		0.1978	False		,,,				2504	0.2791				p.R294R		Atlas-SNP	.											LILRA4,NS,carcinoma,0,1	LILRA4	91	1	0			c.A882G						scavenged	.	T		199,4207		5,189,2009	32.0	32.0	32.0		882	-0.7	0.0	19	dbSNP_121	32	1570,7030		144,1282,2874	no	coding-synonymous	LILRA4	NM_012276.3		149,1471,4883	CC,CT,TT		18.2558,4.5166,13.6014		294/500	54848741	1769,11237	2203	4300	6503	SO:0001819	synonymous_variant	23547	exon5			GTAGCATCTGTAC	AF041261	CCDS12890.1	19q13.4	2013-01-11			ENSG00000239961	ENSG00000239961		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	15503	protein-coding gene	gene with protein product		607517				10941842	Standard	NM_012276		Approved	ILT7, CD85g	uc002qfj.3	P59901	OTTHUMG00000065355	ENST00000291759.4:c.882A>G	19.37:g.54848741T>C		Somatic	157	1	0.00636943		WXS	Illumina HiSeq	Phase_I	153	6	0.0392157	NM_012276	Q32MC4	Silent	SNP	ENST00000291759.4	37	CCDS12890.1																																																																																			T|0.855;C|0.145	0.145	strong		0.692	LILRA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140229.2	NM_012276	
MUC2	4583	hgsc.bcm.edu	37	11	1093296	1093296	+	Silent	SNP	T	T	C	rs200837746|rs56068864		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr11:1093296T>C	ENST00000441003.2	+	30	5142	c.5115T>C	c.(5113-5115)acT>acC	p.T1705T	MUC2_ENST00000333592.6_5'Flank|MUC2_ENST00000359061.5_Silent_p.T1672T|MUC2_ENST00000361558.6_Intron	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)	ccaccaccactacggtgaccc	0.642																																					p.T1705T		Atlas-SNP	.											MUC2_ENST00000441003,rectum,carcinoma,+1,2	MUC2	614	2	0			c.T5115C						scavenged	.						111.0	159.0	142.0					11																	1093296		1883	3466	5349	SO:0001819	synonymous_variant	4583	exon30			CACCACTACGGTG	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.5115T>C	11.37:g.1093296T>C		Somatic	43	11	0.255814		WXS	Illumina HiSeq	Phase_I	65	15	0.230769	NM_002457	Q14878	Silent	SNP	ENST00000441003.2	37																																																																																				.	.	weak		0.642	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
COL15A1	1306	hgsc.bcm.edu	37	9	101831995	101831995	+	Missense_Mutation	SNP	G	G	A	rs10519	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr9:101831995G>A	ENST00000375001.3	+	42	4417	c.3994G>A	c.(3994-3996)Gtc>Atc	p.V1332I		NM_001855.3	NP_001846.3	P39059	COFA1_HUMAN	collagen, type XV, alpha 1	1332	Nonhelical region 10 (NC10).		V -> I (in dbSNP:rs10519).		angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|cell differentiation (GO:0030154)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|signal transduction (GO:0007165)	collagen type XV trimer (GO:0005582)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(20)|liver(1)|lung(42)|ovary(6)|prostate(5)|skin(6)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	107		Acute lymphoblastic leukemia(62;0.0562)				CCCCCATGGCGTCCGCCTTGT	0.502													g|||	914	0.182508	0.2602	0.1153	5008	,	,		17520	0.2758		0.0596	False		,,,				2504	0.1554				p.V1332I		Atlas-SNP	.											COL15A1,colon,carcinoma,0,1	COL15A1	211	1	0			c.G3994A						scavenged	.	A	ILE/VAL	1056,3350	387.0+/-326.3	123,810,1270	110.0	115.0	113.0		3994	2.9	0.4	9	dbSNP_52	113	537,8063	149.4+/-204.5	13,511,3776	yes	missense	COL15A1	NM_001855.3	29	136,1321,5046	AA,AG,GG		6.2442,23.9673,12.2482	benign	1332/1389	101831995	1593,11413	2203	4300	6503	SO:0001583	missense	1306	exon42			CATGGCGTCCGCC	L25286	CCDS35081.1	9q21-q22	2013-01-16			ENSG00000204291	ENSG00000204291		"""Proteoglycans / Extracellular Matrix : Collagen proteoglycans"", ""Collagens"""	2192	protein-coding gene	gene with protein product	"""collagen type XV proteoglycan"""	120325				1427836	Standard	NM_001855		Approved		uc004azb.2	P39059	OTTHUMG00000020351	ENST00000375001.3:c.3994G>A	9.37:g.101831995G>A	ENSP00000364140:p.Val1332Ile	Somatic	112	1	0.00892857		WXS	Illumina HiSeq	Phase_I	137	3	0.0218978	NM_001855	Q5T6J4|Q9UDC5|Q9Y4W4	Missense_Mutation	SNP	ENST00000375001.3	37	CCDS35081.1	359	0.16437728937728938	124	0.25203252032520324	41	0.1132596685082873	144	0.2517482517482518	50	0.06596306068601583	g	8.198	0.797528	0.16327	0.239673	0.062442	ENSG00000204291	ENST00000375001	T	0.42513	0.97	6.17	2.94	0.34122	Collagenase NC10/endostatin (1);C-type lectin fold (1);C-type lectin-like (1);	0.214980	0.47455	N	0.000235	T	0.00012	0.0000	N	0.04636	-0.2	0.80722	P	0.0	B	0.09022	0.002	B	0.06405	0.002	T	0.32268	-0.9913	9	0.07644	T	0.81	-12.17	4.5283	0.11992	0.4105:0.1596:0.4299:0.0	rs10519;rs1051089;rs3191468;rs11541244;rs57446173	1332	P39059	COFA1_HUMAN	I	1332	ENSP00000364140:V1332I	ENSP00000364140:V1332I	V	+	1	0	COL15A1	100871816	0.011000	0.17503	0.390000	0.26220	0.054000	0.15201	0.279000	0.18771	0.449000	0.26747	-0.713000	0.03633	GTC	G|0.860;A|0.140	0.140	strong		0.502	COL15A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053386.3	NM_001855	
PPP1R26	9858	hgsc.bcm.edu	37	9	138376649	138376649	+	Missense_Mutation	SNP	T	T	C	rs3748192	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr9:138376649T>C	ENST00000356818.2	+	4	842	c.293T>C	c.(292-294)gTc>gCc	p.V98A	PPP1R26_ENST00000602993.1_Intron|PPP1R26_ENST00000604351.1_Missense_Mutation_p.V98A|PPP1R26_ENST00000401470.3_Missense_Mutation_p.V98A|PPP1R26_ENST00000605286.1_Missense_Mutation_p.V98A|PPP1R26_ENST00000605660.1_Missense_Mutation_p.V98A	NM_014811.3	NP_055626.3	Q5T8A7	PPR26_HUMAN	protein phosphatase 1, regulatory subunit 26	98			V -> A (in dbSNP:rs3748192). {ECO:0000269|PubMed:15489334}.		negative regulation of phosphatase activity (GO:0010923)	nucleus (GO:0005634)	phosphatase binding (GO:0019902)|protein phosphatase inhibitor activity (GO:0004864)										GCGTTGGCTGTCTGTGGTCTC	0.627													C|||	2095	0.418331	0.2905	0.4899	5008	,	,		16315	0.6528		0.2117	False		,,,				2504	0.5112				p.V98A		Atlas-SNP	.											KIAA0649,NS,carcinoma,0,1	.	.	1	0			c.T293C						PASS	.	C	ALA/VAL	1113,3291		132,849,1221	41.0	48.0	46.0		293	3.4	0.1	9	dbSNP_107	46	1777,6821		195,1387,2717	no	missense	KIAA0649	NM_014811.3	64	327,2236,3938	CC,CT,TT		20.6676,25.2725,22.2273	benign	98/1210	138376649	2890,10112	2202	4299	6501	SO:0001583	missense	9858	exon4			TGGCTGTCTGTGG	AB014549	CCDS6988.1	9q34.3	2012-04-17	2011-10-11	2011-10-11	ENSG00000196422	ENSG00000196422		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	29089	protein-coding gene	gene with protein product	"""DRIM/UTP20 interacting protein"", ""1A6/DRIM (down-regulated in metastasis) interacting protein"""	614056	"""KIAA0649"""	KIAA0649		9734811, 16053918	Standard	NM_014811		Approved		uc004cfr.1	Q5T8A7	OTTHUMG00000020904	ENST00000356818.2:c.293T>C	9.37:g.138376649T>C	ENSP00000349274:p.Val98Ala	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	66	4	0.0606061	NM_014811	Q86WU0|Q8WVV0|Q9Y4D3	Missense_Mutation	SNP	ENST00000356818.2	37	CCDS6988.1	833	0.3814102564102564	122	0.24796747967479674	158	0.43646408839779005	394	0.6888111888111889	159	0.20976253298153033	C	0.007	-2.011636	0.00422	0.252725	0.206676	ENSG00000196422	ENST00000356818;ENST00000401470	T;T	0.46063	0.88;0.88	4.39	3.41	0.39046	.	0.854487	0.10136	N	0.711490	T	0.00012	0.0000	N	0.00289	-1.7	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.45116	-0.9283	9	0.02654	T	1	-12.6961	7.3836	0.26870	0.2105:0.6922:0.0:0.0973	rs3748192;rs17846422;rs17859468;rs3748192	98	Q5T8A7	PPR26_HUMAN	A	98	ENSP00000349274:V98A;ENSP00000385826:V98A	ENSP00000349274:V98A	V	+	2	0	KIAA0649	137516470	0.006000	0.16342	0.106000	0.21319	0.067000	0.16453	1.185000	0.32065	1.085000	0.41206	-0.119000	0.15052	GTC	T|0.723;C|0.277	0.277	strong		0.627	PPP1R26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054987.1	NM_014811	
HLA-C	3107	hgsc.bcm.edu	37	6	31239613	31239613	+	Missense_Mutation	SNP	C	C	T	rs2308538	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr6:31239613C>T	ENST00000376228.5	-	2	120	c.106G>A	c.(106-108)Gtg>Atg	p.V36M	HLA-C_ENST00000383329.3_Missense_Mutation_p.V36M	NM_002117.5	NP_002108.4	Q95604	1C17_HUMAN	major histocompatibility complex, class I, C	36	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)	peptide antigen binding (GO:0042605)	p.V36M(2)		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						GGCCGGGACACGGCGGTGTCG	0.721																																					p.V36M		Atlas-SNP	.											HLA-C_ENST00000383329,NS,carcinoma,0,2	HLA-C	92	2	2	Substitution - Missense(2)	prostate(2)	c.G106A						scavenged	.						19.0	19.0	19.0					6																	31239613		1490	2687	4177	SO:0001583	missense	3107	exon2			GGGACACGGCGGT	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.106G>A	6.37:g.31239613C>T	ENSP00000365402:p.Val36Met	Somatic	76	3	0.0394737		WXS	Illumina HiSeq	Phase_I	120	6	0.05	NM_002117	O02864|O02958|Q29643|Q9MY30	Missense_Mutation	SNP	ENST00000376228.5	37	CCDS34393.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	N|N	13.07|13.07	2.127655|2.127655	0.37533|0.37533	.|.	.|.	ENSG00000204525|ENSG00000204525	ENST00000415537|ENST00000376228;ENST00000383329;ENST00000396254;ENST00000539307	.|T;T	.|0.01092	.|5.35;5.35	2.16|2.16	2.16|2.16	0.27623|0.27623	.|MHC class I, alpha chain, alpha1/alpha2 (1);MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);	.|0.224693	.|0.20953	.|U	.|0.082710	T|T	0.01661|0.01661	0.0053|0.0053	M|M	0.63843|0.63843	1.955|1.955	0.23747|0.23747	N|N	0.996957|0.996957	.|D;D;D;D	.|0.89917	.|1.0;1.0;1.0;1.0	.|D;D;D;D	.|0.97110	.|0.999;0.999;0.999;1.0	T|T	0.53236|0.53236	-0.8467|-0.8467	5|10	.|0.30854	.|T	.|0.27	.|.	7.8706|7.8706	0.29563|0.29563	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|36;36;36;36	.|A2AEA4;A6H578;A2AEA2;P10321	.|.;.;.;1C07_HUMAN	H|M	35|36;36;36;73	.|ENSP00000365402:V36M;ENSP00000372819:V36M	.|ENSP00000365402:V36M	R|V	-|-	2|1	0|0	HLA-C|HLA-C	31347592|31347592	0.000000|0.000000	0.05858|0.05858	0.780000|0.780000	0.31762|0.31762	0.007000|0.007000	0.05969|0.05969	0.465000|0.465000	0.22004|0.22004	1.524000|1.524000	0.49035|0.49035	0.305000|0.305000	0.20034|0.20034	CGT|GTG	T|0.155;C|0.845	0.155	strong		0.721	HLA-C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076281.3	NM_002117	
OR4N4	283694	hgsc.bcm.edu	37	15	22383066	22383066	+	Silent	SNP	A	A	G	rs559754|rs67576397	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr15:22383066A>G	ENST00000328795.4	+	1	685	c.594A>G	c.(592-594)ctA>ctG	p.L198L	RP11-69H14.6_ENST00000558896.1_RNA	NM_001005241.2	NP_001005241.2	Q8N0Y3	OR4N4_HUMAN	olfactory receptor, family 4, subfamily N, member 4	198						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(3)|kidney(3)|large_intestine(6)|lung(19)|ovary(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	40		all_cancers(20;1.94e-20)|all_epithelial(15;3.94e-18)|Lung NSC(15;8.53e-15)|all_lung(15;2.87e-14)|Breast(32;0.00519)|Colorectal(260;0.101)	GBM - Glioblastoma multiforme(6;0.124)	all cancers(64;1.64e-11)|Epithelial(43;5.81e-10)|BRCA - Breast invasive adenocarcinoma(123;0.000255)|Kidney(6;0.00736)|KIRC - Kidney renal clear cell carcinoma(6;0.0135)|GBM - Glioblastoma multiforme(186;0.0963)		TGGAGCTTCTAATGGTCTTCA	0.522													g|||	2105	0.420327	0.4297	0.3862	5008	,	,		25329	0.4127		0.4642	False		,,,				2504	0.3947				p.L198L		Atlas-SNP	.											OR4N4,colon,carcinoma,+2,1	OR4N4	108	1	0			c.A594G						scavenged	.						121.0	97.0	105.0					15																	22383066		2190	4259	6449	SO:0001819	synonymous_variant	283694	exon1			GCTTCTAATGGTC	AI018459	CCDS32173.1	15q11.2	2012-08-09				ENSG00000183706		"""GPCR / Class A : Olfactory receptors"""	15375	protein-coding gene	gene with protein product							Standard	NM_001005241		Approved		uc010tzv.2	Q8N0Y3		ENST00000328795.4:c.594A>G	15.37:g.22383066A>G		Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	132	4	0.030303	NM_001005241	Q6IEY3|Q6IF56	Silent	SNP	ENST00000328795.4	37	CCDS32173.1																																																																																			ATG|0.500;CTA|0.500	.	alt		0.522	OR4N4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414922.1		
PSG11	5680	hgsc.bcm.edu	37	19	43519270	43519270	+	Missense_Mutation	SNP	A	A	G	rs111493043	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr19:43519270A>G	ENST00000401740.1	-	4	1065	c.962T>C	c.(961-963)aTt>aCt	p.I321T	PSG11_ENST00000403486.1_Missense_Mutation_p.I199T|PSG11_ENST00000320078.7_Missense_Mutation_p.I321T|PSG11_ENST00000595312.1_5'Flank|PSG11_ENST00000306322.7_Missense_Mutation_p.I199T			Q00887	PSG9_HUMAN	pregnancy specific beta-1-glycoprotein 11	414	Ig-like C2-type 2.				female pregnancy (GO:0007565)	extracellular region (GO:0005576)		p.I321T(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(15)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	26		Prostate(69;0.00682)				CCACTTACCAATGACTCTGAT	0.463													.|||	184	0.0367412	0.0287	0.0029	5008	,	,		21410	0.0883		0.0	False		,,,				2504	0.0562				p.I321T		Atlas-SNP	.											PSG11,NS,carcinoma,0,1	PSG11	57	1	1	Substitution - Missense(1)	stomach(1)	c.T962C						scavenged	.	A	THR/ILE,THR/ILE,THR/ILE	140,4258	99.8+/-138.5	10,120,2069	138.0	132.0	134.0		596,962,596	-2.0	0.0	19	dbSNP_132	134	16,8580	11.2+/-40.8	0,16,4282	yes	missense,missense,missense	PSG11	NM_001113410.1,NM_002785.2,NM_203287.1	89,89,89	10,136,6351	GG,GA,AA		0.1861,3.1833,1.2006	,,	199/214,321/336,199/214	43519270	156,12838	2199	4298	6497	SO:0001583	missense	5680	exon4			TTACCAATGACTC	U25988	CCDS12614.2, CCDS12615.2	19q13.2	2013-01-29			ENSG00000243130	ENSG00000243130		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9516	protein-coding gene	gene with protein product	"""pregnancy specific beta-1-glycoprotein 13"""	176401		PSG13, PSG14		7794280	Standard	NM_001113410		Approved	MGC22484	uc002ovm.1	Q9UQ72	OTTHUMG00000151546	ENST00000401740.1:c.962T>C	19.37:g.43519270A>G	ENSP00000384995:p.Ile321Thr	Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	148	5	0.0337838	NM_002785	B2R869|Q15227|Q15236|Q15237|Q8WW78|Q9UQ73	Missense_Mutation	SNP	ENST00000401740.1	37	CCDS12614.2	68	0.031135531135531136	18	0.036585365853658534	0	0.0	50	0.08741258741258741	0	0.0	a	0.012	-1.679652	0.00751	0.031833	0.001861	ENSG00000243130	ENST00000320078;ENST00000403486;ENST00000306322;ENST00000401740	T;T;T;T	0.72282	-0.64;-0.64;-0.64;-0.64	0.976	-1.95	0.07548	Immunoglobulin-like fold (1);	.	.	.	.	T	0.01558	0.0050	N	0.02539	-0.55	0.09310	N	1	B;B	0.13594	0.004;0.008	B;B	0.15484	0.012;0.013	T	0.02020	-1.1228	9	0.29301	T	0.29	.	2.7499	0.05277	0.2605:0.0:0.4834:0.2561	.	199;321	Q9UQ72-2;Q9UQ72	.;PSG11_HUMAN	T	321;199;199;321	ENSP00000319140:I321T;ENSP00000385427:I199T;ENSP00000304913:I199T;ENSP00000384995:I321T	ENSP00000304913:I199T	I	-	2	0	PSG11	48211110	0.002000	0.14202	0.003000	0.11579	0.005000	0.04900	-1.447000	0.02396	-1.624000	0.01556	-1.386000	0.01163	ATT	A|0.982;G|0.018	0.018	strong		0.463	PSG11-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323079.1	NM_002785	
CTAGE4	100128553	hgsc.bcm.edu	37	7	143882697	143882697	+	Missense_Mutation	SNP	A	A	G	rs145692929	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr7:143882697A>G	ENST00000486333.1	+	1	2139	c.2101A>G	c.(2101-2103)Atc>Gtc	p.I701V		NM_198495.2	NP_940897.2	Q8IX94	CTGE4_HUMAN	CTAGE family, member 4	701	Pro-rich.			IS -> VR (in Ref. 1; BAF84925). {ECO:0000305}.		integral component of membrane (GO:0016021)				endometrium(1)|ovary(2)	3						TCTTGCTCCAATCAGCGGTCC	0.507																																					p.I701V		Atlas-SNP	.											CTAGE4,right_upper_lobe,carcinoma,-2,1	CTAGE4	10	1	0			c.A2101G						scavenged	.						5.0	8.0	7.0					7																	143882697		623	1434	2057	SO:0001583	missense	100128553	exon1			GCTCCAATCAGCG	AF338232	CCDS55176.1	7q35	2009-10-15			ENSG00000225932	ENSG00000225932			24772	protein-coding gene	gene with protein product	"""cutaneous T-cell lymphoma-associated antigen 4"""	608910				12839582, 11149944	Standard	NM_198495		Approved	FLJ43692, cTAGE-4	uc010lpc.3	Q8IX94	OTTHUMG00000157997	ENST00000486333.1:c.2101A>G	7.37:g.143882697A>G	ENSP00000419539:p.Ile701Val	Somatic	112	1	0.00892857		WXS	Illumina HiSeq	Phase_I	112	8	0.0714286	NM_198495	A8K871|O95046	Missense_Mutation	SNP	ENST00000486333.1	37	CCDS55176.1	.	.	.	.	.	.	.	.	.	.	.	1.245	-0.620260	0.03636	.	.	ENSG00000225932	ENST00000486333	T	0.05513	3.43	.	.	.	.	.	.	.	.	T	0.03011	0.0089	N	0.17248	0.465	0.09310	N	1	B	0.02656	0.0	B	0.10450	0.005	T	0.46857	-0.9161	7	0.02654	T	1	.	.	.	.	.	701	Q8IX94	CTGE4_HUMAN	V	701	ENSP00000419539:I701V	ENSP00000419539:I701V	I	+	1	0	CTAGE4	143513630	0.921000	0.31238	0.013000	0.15412	0.013000	0.08279	0.158000	0.16422	0.149000	0.19098	0.147000	0.16070	ATC	A|0.500;G|0.500	0.500	strong		0.507	CTAGE4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349970.1	NM_198495	
GSG2	83903	hgsc.bcm.edu	37	17	3628212	3628212	+	Missense_Mutation	SNP	T	T	C	rs220461	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr17:3628212T>C	ENST00000325418.4	+	1	1002	c.983T>C	c.(982-984)aTa>aCa	p.I328T	ITGAE_ENST00000263087.4_Intron|CTD-3195I5.3_ENST00000571741.1_RNA|ITGAE_ENST00000571185.1_Intron	NM_031965.2	NP_114171.2	Q8TF76	HASP_HUMAN	germ cell associated 2 (haspin)	328			I -> T (in dbSNP:rs220461). {ECO:0000269|PubMed:11311556, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17344846}.		histone H3-T3 phosphorylation involved in chromosome passenger complex localization to kinetochore (GO:2000751)|intracellular signal transduction (GO:0035556)|mitotic sister chromatid cohesion (GO:0007064)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|protein localization to chromosome, centromeric region (GO:0071459)|protein phosphorylation (GO:0006468)|regulation of spindle checkpoint (GO:0090231)	centrosome (GO:0005813)|chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|spindle (GO:0005819)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|histone kinase activity (H3-T3 specific) (GO:0072354)|protein kinase activity (GO:0004672)										CCAAGGGGAATAGACAGGCTG	0.552													T|||	1270	0.253594	0.0219	0.1556	5008	,	,		19545	0.3006		0.3072	False		,,,				2504	0.5327				p.I328T		Atlas-SNP	.											.	GSG2	48	.	0			c.T983C						PASS	.	T	,THR/ILE	309,4097	162.2+/-194.2	17,275,1911	55.0	51.0	52.0		,983	-8.7	0.0	17	dbSNP_79	52	2743,5857	426.7+/-355.4	435,1873,1992	yes	intron,missense	ITGAE,GSG2	NM_002208.4,NM_031965.2	,89	452,2148,3903	CC,CT,TT		31.8953,7.0132,23.4661	,benign	,328/799	3628212	3052,9954	2203	4300	6503	SO:0001583	missense	83903	exon1			GGGGAATAGACAG	AB039834	CCDS11036.1	17p13	2005-01-19			ENSG00000177602	ENSG00000177602			19682	protein-coding gene	gene with protein product		609240					Standard	NM_031965		Approved	haspin	uc002fwp.3	Q8TF76	OTTHUMG00000090703	ENST00000325418.4:c.983T>C	17.37:g.3628212T>C	ENSP00000325290:p.Ile328Thr	Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	50	4	0.08	NM_031965	Q5U5K3|Q96MN1|Q9BXS7	Missense_Mutation	SNP	ENST00000325418.4	37	CCDS11036.1	494	0.2261904761904762	15	0.03048780487804878	65	0.17955801104972377	177	0.3094405594405594	237	0.31266490765171506	T	1.096	-0.662582	0.03454	0.070132	0.318953	ENSG00000177602	ENST00000325418	T	0.06933	3.24	4.33	-8.67	0.00863	.	0.902637	0.09044	N	0.856810	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B	0.06786	0.001	B	0.01281	0.0	T	0.49688	-0.8913	9	0.87932	D	0	-23.7501	9.806	0.40792	0.1041:0.6357:0.1141:0.1461	rs220461;rs3809807;rs17463403;rs58374758;rs220461	328	Q8TF76	HASP_HUMAN	T	328	ENSP00000325290:I328T	ENSP00000325290:I328T	I	+	2	0	GSG2	3574961	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.294000	0.01144	-2.050000	0.00905	-1.064000	0.02280	ATA	T|0.769;C|0.230	0.230	strong		0.552	GSG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207391.1	NM_031965	
INTU	27152	hgsc.bcm.edu	37	4	128628100	128628100	+	Missense_Mutation	SNP	A	A	C	rs35858752	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr4:128628100A>C	ENST00000335251.6	+	12	2350	c.2247A>C	c.(2245-2247)ttA>ttC	p.L749F		NM_015693.3	NP_056508.2	Q9ULD6	INTU_HUMAN	inturned planar cell polarity protein	749					cilium assembly (GO:0042384)|hair follicle morphogenesis (GO:0031069)|keratinocyte differentiation (GO:0030216)|limb development (GO:0060173)|negative regulation of cell division (GO:0051782)|negative regulation of keratinocyte proliferation (GO:0010839)|nervous system development (GO:0007399)|positive regulation of smoothened signaling pathway (GO:0045880)|regulation of smoothened signaling pathway (GO:0008589)|spinal cord dorsal/ventral patterning (GO:0021513)	cytoplasm (GO:0005737)				breast(3)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(8)|liver(2)|lung(17)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	43						CTGATGGTTTAGAAGAAAGTG	0.448													A|||	362	0.0722843	0.0	0.0821	5008	,	,		20418	0.2758		0.0199	False		,,,				2504	0.0072				p.L749F		Atlas-SNP	.											.	INTU	92	.	0			c.A2247C						PASS	.	A	PHE/LEU	36,4370	40.0+/-72.8	0,36,2167	195.0	196.0	195.0		2247	-1.9	0.5	4	dbSNP_126	195	113,8487	60.6+/-122.4	0,113,4187	yes	missense	INTU	NM_015693.3	22	0,149,6354	CC,CA,AA		1.314,0.8171,1.1456	benign	749/943	128628100	149,12857	2203	4300	6503	SO:0001583	missense	27152	exon12			TGGTTTAGAAGAA	BC051698	CCDS34061.1	4q28.2	2013-03-05	2013-03-05	2006-10-24	ENSG00000164066	ENSG00000164066			29239	protein-coding gene	gene with protein product		610621	"""PDZ domain containing 6"", ""inturned planar cell polarity effector homolog (Drosophila)"""	PDZK6, PDZD6		10574462, 21761479	Standard	NM_015693		Approved	KIAA1284	uc003ifk.2	Q9ULD6	OTTHUMG00000161202	ENST00000335251.6:c.2247A>C	4.37:g.128628100A>C	ENSP00000334003:p.Leu749Phe	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	110	5	0.0454545	NM_015693	A1L4N5|D6RAE6|D6RBT4|Q4W5I8|Q86V55	Missense_Mutation	SNP	ENST00000335251.6	37	CCDS34061.1	227	0.10393772893772894	0	0.0	29	0.08011049723756906	178	0.3111888111888112	20	0.026385224274406333	A	0.019	-1.461435	0.01062	0.008171	0.01314	ENSG00000164066	ENST00000335251	.	.	.	4.36	-1.85	0.07784	.	1.487300	0.03485	N	0.215726	T	0.00012	0.0000	N	0.22421	0.69	0.09310	P	0.9999999411836	B	0.02656	0.0	B	0.01281	0.0	T	0.28870	-1.0030	8	0.10111	T	0.7	-0.1168	4.2651	0.10759	0.4697:0.0:0.2525:0.2778	rs35858752	749	Q9ULD6	PDZD6_HUMAN	F	749	.	ENSP00000334003:L749F	L	+	3	2	INTU	128847550	0.006000	0.16342	0.452000	0.26994	0.073000	0.16967	0.020000	0.13466	-0.234000	0.09782	0.528000	0.53228	TTA	A|0.963;C|0.037	0.037	strong		0.448	INTU-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364147.2	XM_371707	
UFL1	23376	hgsc.bcm.edu	37	6	96999725	96999725	+	Silent	SNP	C	C	T	rs1127175	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr6:96999725C>T	ENST00000369278.4	+	17	1977	c.1911C>T	c.(1909-1911)gaC>gaT	p.D637D		NM_015323.4	NP_056138.1	O94874	UFL1_HUMAN	UFM1-specific ligase 1	637					negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein ubiquitination (GO:0031397)|osteoblast differentiation (GO:0001649)|protein ufmylation (GO:0071569)|regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032434)|response to endoplasmic reticulum stress (GO:0034976)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nucleus (GO:0005634)	UFM1 conjugating enzyme activity (GO:0071568)										GCATAGAAGACTTTATTTCTT	0.299													C|||	1636	0.326677	0.326	0.2911	5008	,	,		16341	0.3075		0.3698	False		,,,				2504	0.3282				p.D637D		Atlas-SNP	.											KIAA0776,NS,carcinoma,0,2	.	.	2	0			c.C1911T						scavenged	.	C		1470,2934	455.5+/-351.0	239,992,971	86.0	95.0	92.0		1911	-0.4	1.0	6	dbSNP_86	92	2996,5600	455.3+/-363.7	536,1924,1838	no	coding-synonymous	UFL1	NM_015323.4		775,2916,2809	TT,TC,CC		34.8534,33.3787,34.3538		637/795	96999725	4466,8534	2202	4298	6500	SO:0001819	synonymous_variant	23376	exon17			AGAAGACTTTATT	BC036379	CCDS5034.1	6q16.3	2011-08-18	2011-08-18	2011-08-18	ENSG00000014123	ENSG00000014123			23039	protein-coding gene	gene with protein product	"""novel LZAP-binding protein"", ""Regulator of CDK5RAP3 and DDRGK1"""	613372	"""KIAA0776"""	KIAA0776		20018847, 20164180, 20228063, 20531390	Standard	NM_015323		Approved	NLBP, Maxer, RCAD	uc003por.3	O94874	OTTHUMG00000015238	ENST00000369278.4:c.1911C>T	6.37:g.96999725C>T		Somatic	523	3	0.00573614		WXS	Illumina HiSeq	Phase_I	352	10	0.0284091	NM_015323	A0PJ53|B4DJ57|C0H5X5|Q8N765|Q9NTQ0	Silent	SNP	ENST00000369278.4	37	CCDS5034.1																																																																																			C|0.662;T|0.338	0.338	strong		0.299	UFL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041557.1	NM_015323	
NAPEPLD	222236	hgsc.bcm.edu	37	7	102760511	102760511	+	Missense_Mutation	SNP	A	A	C	rs12540583	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr7:102760511A>C	ENST00000417955.1	-	3	608	c.454T>G	c.(454-456)Tct>Gct	p.S152A	NAPEPLD_ENST00000465647.1_Missense_Mutation_p.S152A|NAPEPLD_ENST00000341533.4_Missense_Mutation_p.S152A|NAPEPLD_ENST00000427257.1_Missense_Mutation_p.S152A|NAPEPLD_ENST00000455523.2_Missense_Mutation_p.S225A			Q6IQ20	NAPEP_HUMAN	N-acyl phosphatidylethanolamine phospholipase D	152			S -> A (in dbSNP:rs12540583).		phospholipid catabolic process (GO:0009395)	extracellular vesicular exosome (GO:0070062)|photoreceptor outer segment membrane (GO:0042622)	N-acylphosphatidylethanolamine-specific phospholipase D activity (GO:0070290)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	17						GAAGCACGAGAGCTAAAGATG	0.502													A|||	841	0.167931	0.0946	0.1844	5008	,	,		13891	0.2768		0.0974	False		,,,				2504	0.2157				p.S152A		Atlas-SNP	.											.	NAPEPLD	49	.	0			c.T454G						PASS	.	A	ALA/SER,ALA/SER	364,4042	185.7+/-212.7	12,340,1851	169.0	132.0	144.0		454,454	-4.7	0.1	7	dbSNP_120	144	890,7710	199.9+/-243.8	51,788,3461	yes	missense,missense	NAPEPLD	NM_001122838.1,NM_198990.4	99,99	63,1128,5312	CC,CA,AA		10.3488,8.2615,9.6417	benign,benign	152/394,152/394	102760511	1254,11752	2203	4300	6503	SO:0001583	missense	222236	exon3			CACGAGAGCTAAA	BC037350, AY357337	CCDS5729.1	7q22.1	2014-03-14			ENSG00000161048	ENSG00000161048	3.1.4.54		21683	protein-coding gene	gene with protein product	"""chromosome 7 open reading frame 18, N-acyl-phosphatidylethanolamine-hydrolyzing phospholipase D"""	612334				14634025, 15820312, 18067139	Standard	NM_198990		Approved	FMP30, C7orf18, NAPE-PLD	uc003vbd.2	Q6IQ20	OTTHUMG00000157204	ENST00000417955.1:c.454T>G	7.37:g.102760511A>C	ENSP00000407112:p.Ser152Ala	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	116	5	0.0431034	NM_001122838	Q5CZ87|Q769K1	Missense_Mutation	SNP	ENST00000417955.1	37	CCDS5729.1	347	0.15888278388278387	60	0.12195121951219512	58	0.16022099447513813	159	0.27797202797202797	70	0.09234828496042216	A	13.41	2.228637	0.39399	0.082615	0.103488	ENSG00000161048	ENST00000341533;ENST00000417955;ENST00000465647;ENST00000427257;ENST00000455523	D;D;D;D;D	0.91792	-2.91;-2.91;-2.91;-2.91;-2.91	5.93	-4.69	0.03299	.	0.645957	0.17297	N	0.179417	T	0.00039	0.0001	N	0.25332	0.735	0.48762	P	2.9800000000002047E-4	B;B	0.06786	0.001;0.0	B;B	0.15052	0.012;0.002	T	0.16660	-1.0395	9	0.44086	T	0.13	-5.2249	2.2767	0.04104	0.1181:0.2271:0.3677:0.2871	rs12540583;rs12540583	225;152	B4E3B0;Q6IQ20	.;NAPEP_HUMAN	A	152;152;152;152;225	ENSP00000340093:S152A;ENSP00000407112:S152A;ENSP00000419188:S152A;ENSP00000392775:S152A;ENSP00000414364:S225A	ENSP00000340093:S152A	S	-	1	0	NAPEPLD	102547747	1.000000	0.71417	0.065000	0.19835	0.998000	0.95712	1.650000	0.37292	-0.455000	0.07054	0.482000	0.46254	TCT	A|0.876;C|0.124	0.124	strong		0.502	NAPEPLD-002	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347904.1	NM_198990	
MUC4	4585	hgsc.bcm.edu	37	3	195506007	195506007	+	Silent	SNP	G	G	A			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr3:195506007G>A	ENST00000463781.3	-	2	12903	c.12444C>T	c.(12442-12444)acC>acT	p.T4148T	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Silent_p.T4148T	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.T4148T(2)		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)		AGGAAGGGATGGTGACAGGAA	0.587																																					p.T4148T		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	2	Substitution - coding silent(2)	kidney(1)|endometrium(1)	c.C12444T						scavenged	.						40.0	22.0	27.0					3																	195506007		646	1562	2208	SO:0001819	synonymous_variant	4585	exon2			AGGGATGGTGACA	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.12444C>T	3.37:g.195506007G>A		Somatic	32	4	0.125		WXS	Illumina HiSeq	Phase_I	31	6	0.193548	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|1.000;|0.000	.	weak		0.587	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
PCDHB7	56129	hgsc.bcm.edu	37	5	140553994	140553994	+	Silent	SNP	G	G	T	rs374392843		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr5:140553994G>T	ENST00000231137.3	+	1	1752	c.1578G>T	c.(1576-1578)gcG>gcT	p.A526A		NM_018940.2	NP_061763.1	Q9Y5E2	PCDB7_HUMAN	protocadherin beta 7	526	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)	p.A526A(1)		NS(2)|breast(2)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(20)|lung(54)|ovary(5)|prostate(7)|skin(7)|upper_aerodigestive_tract(4)|urinary_tract(1)	119			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CCCTGCAGGCGTTCGAGTTCC	0.706													g|||	1	0.000199681	0.0	0.0	5008	,	,		16269	0.0		0.001	False		,,,				2504	0.0				p.A526A		Atlas-SNP	.											PCDHB7,NS,carcinoma,0,4	PCDHB7	231	4	1	Substitution - coding silent(1)	lung(1)	c.G1578T						scavenged	.						62.0	68.0	66.0					5																	140553994		2203	4300	6503	SO:0001819	synonymous_variant	56129	exon1			GCAGGCGTTCGAG	AF152500	CCDS4249.1	5q31	2010-01-26			ENSG00000113212	ENSG00000113212		"""Cadherins / Protocadherins : Clustered"""	8692	other	protocadherin		606333				10380929	Standard	NM_018940		Approved	PCDH-BETA7	uc003lit.3	Q9Y5E2	OTTHUMG00000129608	ENST00000231137.3:c.1578G>T	5.37:g.140553994G>T		Somatic	218	3	0.0137615		WXS	Illumina HiSeq	Phase_I	233	6	0.0257511	NM_018940	A1L3Y8	Silent	SNP	ENST00000231137.3	37	CCDS4249.1																																																																																			.	.	weak		0.706	PCDHB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251803.2	NM_018940	
BCL10	8915	hgsc.bcm.edu	37	1	85736460	85736460	+	Missense_Mutation	SNP	T	T	G			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr1:85736460T>G	ENST00000370580.1	-	2	924	c.187A>C	c.(187-189)Aaa>Caa	p.K63Q		NM_003921.4	NP_003912.1	O95999	BCL10_HUMAN	B-cell CLL/lymphoma 10	63	CARD. {ECO:0000255|PROSITE- ProRule:PRU00046}.				adaptive immune response (GO:0002250)|B cell apoptotic process (GO:0001783)|cell death (GO:0008219)|cellular defense response (GO:0006968)|cellular response to mechanical stimulus (GO:0071260)|Fc-epsilon receptor signaling pathway (GO:0038095)|immunoglobulin mediated immune response (GO:0016064)|innate immune response (GO:0045087)|interleukin-6 biosynthetic process (GO:0042226)|lymphotoxin A biosynthetic process (GO:0042109)|negative regulation of mature B cell apoptotic process (GO:0002906)|neural tube closure (GO:0001843)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-8 biosynthetic process (GO:0045416)|positive regulation of mast cell cytokine production (GO:0032765)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of T cell activation (GO:0050870)|positive regulation of transcription, DNA-templated (GO:0045893)|protein homooligomerization (GO:0051260)|protein oligomerization (GO:0051259)|regulation of T cell receptor signaling pathway (GO:0050856)|response to food (GO:0032094)|response to fungus (GO:0009620)|response to molecule of bacterial origin (GO:0002237)|T cell apoptotic process (GO:0070231)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor signaling pathway (GO:0002224)	CBM complex (GO:0032449)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|immunological synapse (GO:0001772)|lysosome (GO:0005764)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	enzyme binding (GO:0019899)|kinase binding (GO:0019900)|NF-kappaB binding (GO:0051059)|protease binding (GO:0002020)|protein C-terminus binding (GO:0008022)|protein kinase B binding (GO:0043422)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)			haematopoietic_and_lymphoid_tissue(7)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|stomach(1)|urinary_tract(1)	19				all cancers(265;0.0114)|Epithelial(280;0.0311)		CCAGCCCTTTTTCTACTTGAT	0.373			T	IGH@	MALT																																p.K63Q	NSCLC(34;993 1034 12176 32621 50182)	Atlas-SNP	.		Dom	yes		1	1p22	8915	B-cell CLL/lymphoma 10		L	.	BCL10	39	.	0			c.A187C						PASS	.						110.0	114.0	113.0					1																	85736460		2203	4300	6503	SO:0001583	missense	8915	exon2			CCCTTTTTCTACT	AJ006288	CCDS704.1	1p22	2008-07-18			ENSG00000142867	ENSG00000142867			989	protein-coding gene	gene with protein product	"""CARD-like apoptotic protein"", ""CARD-containing apoptotic signaling protein"", ""CARD containing molecule enhancing NF-kB"", ""caspase-recruiting domain-containing protein"", ""CARD-containing proapoptotic protein"""	603517				9989495	Standard	NM_003921		Approved	CARMEN, CIPER, mE10, c-E10, CLAP	uc021opd.1	O95999	OTTHUMG00000009965	ENST00000370580.1:c.187A>C	1.37:g.85736460T>G	ENSP00000359612:p.Lys63Gln	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	154	71	0.461039	NM_003921	Q5VUF1	Missense_Mutation	SNP	ENST00000370580.1	37	CCDS704.1	.	.	.	.	.	.	.	.	.	.	T	22.1	4.250050	0.80024	.	.	ENSG00000142867	ENST00000370580;ENST00000271015;ENST00000394761	T	0.20463	2.07	5.69	5.69	0.88448	DEATH-like (2);Caspase Recruitment (2);	0.048742	0.85682	D	0.000000	T	0.29620	0.0739	L	0.53249	1.67	0.42293	D	0.992143	D	0.76494	0.999	D	0.68483	0.958	T	0.04509	-1.0946	10	0.66056	D	0.02	-31.1976	12.1424	0.54005	0.0:0.0:0.1427:0.8573	.	63	O95999	BCL10_HUMAN	Q	63	ENSP00000359612:K63Q	ENSP00000271015:K63Q	K	-	1	0	BCL10	85509048	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	4.576000	0.60915	2.291000	0.77112	0.533000	0.62120	AAA	.	.	none		0.373	BCL10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027612.1	NM_003921	
OR2M5	127059	hgsc.bcm.edu	37	1	248309020	248309020	+	Missense_Mutation	SNP	G	G	A	rs139290187	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr1:248309020G>A	ENST00000366476.1	+	1	571	c.571G>A	c.(571-573)Gac>Aac	p.D191N		NM_001004690.1	NP_001004690.1	A3KFT3	OR2M5_HUMAN	olfactory receptor, family 2, subfamily M, member 5	191						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|endometrium(5)|kidney(2)|large_intestine(7)|liver(1)|lung(25)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	49	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;0.0388)			CTCATGCAATGACACATCAAT	0.418																																					p.D191N		Atlas-SNP	.											OR2M5,NS,carcinoma,0,2	OR2M5	117	2	0			c.G571A						scavenged	.						284.0	272.0	276.0					1																	248309020		2203	4300	6503	SO:0001583	missense	127059	exon1			TGCAATGACACAT		CCDS31105.1	1q44	2012-08-09		2004-03-10	ENSG00000162727	ENSG00000162727		"""GPCR / Class A : Olfactory receptors"""	19576	protein-coding gene	gene with protein product				OR2M5P			Standard	NM_001004690		Approved		uc010pze.2	A3KFT3	OTTHUMG00000040447	ENST00000366476.1:c.571G>A	1.37:g.248309020G>A	ENSP00000355432:p.Asp191Asn	Somatic	201	0	0		WXS	Illumina HiSeq	Phase_I	253	8	0.0316206	NM_001004690		Missense_Mutation	SNP	ENST00000366476.1	37	CCDS31105.1	.	.	.	.	.	.	.	.	.	.	g	13.27	2.186763	0.38609	.	.	ENSG00000162727	ENST00000366476	T	0.00231	8.49	3.05	-0.584	0.11702	GPCR, rhodopsin-like superfamily (1);	0.000000	0.33691	U	0.004660	T	0.00178	0.0005	M	0.63843	1.955	0.09310	N	1	B	0.20052	0.041	B	0.25405	0.06	T	0.40739	-0.9547	10	0.52906	T	0.07	.	6.3472	0.21355	0.2028:0.2355:0.5617:0.0	.	191	A3KFT3	OR2M5_HUMAN	N	191	ENSP00000355432:D191N	ENSP00000355432:D191N	D	+	1	0	OR2M5	246375643	0.002000	0.14202	0.001000	0.08648	0.566000	0.35808	0.608000	0.24223	-0.004000	0.14419	0.492000	0.49549	GAC	G|0.996;A|0.004	0.004	strong		0.418	OR2M5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097343.1	NM_001004690	
ZNF418	147686	hgsc.bcm.edu	37	19	58439306	58439306	+	Silent	SNP	G	G	A	rs7253514	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr19:58439306G>A	ENST00000396147.1	-	4	534	c.243C>T	c.(241-243)gcC>gcT	p.A81A	ZNF418_ENST00000599852.1_5'UTR|ZNF418_ENST00000600989.1_Intron|ZNF418_ENST00000599086.1_5'Flank|ZNF418_ENST00000425570.3_Silent_p.A102A|ZNF418_ENST00000595830.1_Silent_p.A81A	NM_133460.1	NP_597717.1	Q8TF45	ZN418_HUMAN	zinc finger protein 418	81	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)			cervix(1)|endometrium(6)|kidney(1)|large_intestine(6)|lung(9)|prostate(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	31		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;0.0158)		CACAAGAGTGGGCCTTCTTGG	0.507													G|||	1448	0.289137	0.2595	0.3573	5008	,	,		18775	0.4048		0.2545	False		,,,				2504	0.1973				p.A81A		Atlas-SNP	.											.	ZNF418	76	.	0			c.C243T						PASS	.	G		1066,3340		131,804,1268	62.0	66.0	64.0		243	-1.5	0.0	19	dbSNP_116	64	2219,6381		293,1633,2374	no	coding-synonymous	ZNF418	NM_133460.1		424,2437,3642	AA,AG,GG		25.8023,24.1943,25.2576		81/677	58439306	3285,9721	2203	4300	6503	SO:0001819	synonymous_variant	147686	exon4			AGAGTGGGCCTTC	AB075836, AY695825	CCDS42642.1	19q13.43	2013-01-08				ENSG00000196724		"""Zinc fingers, C2H2-type"", ""-"""	20647	protein-coding gene	gene with protein product						11853319	Standard	NM_133460		Approved	KIAA1956, FLJ31551	uc002qqs.1	Q8TF45		ENST00000396147.1:c.243C>T	19.37:g.58439306G>A		Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	179	8	0.0446927	NM_133460	Q2M1S2|Q670L5|Q96N18	Silent	SNP	ENST00000396147.1	37	CCDS42642.1																																																																																			G|0.704;A|0.296	0.296	strong		0.507	ZNF418-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466693.1	NM_133460	
LAP3	51056	hgsc.bcm.edu	37	4	17586703	17586703	+	Silent	SNP	T	T	C	rs3733576	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr4:17586703T>C	ENST00000226299.4	+	6	922	c.648T>C	c.(646-648)gcT>gcC	p.A216A	AC006160.5_ENST00000511010.1_RNA|LAP3_ENST00000606142.1_Silent_p.A185A	NM_015907.2	NP_056991.2	P28838	AMPL_HUMAN	leucine aminopeptidase 3	216					proteolysis (GO:0006508)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|trans-Golgi network (GO:0005802)	aminopeptidase activity (GO:0004177)|manganese ion binding (GO:0030145)|metalloexopeptidase activity (GO:0008235)			endometrium(4)|kidney(1)|large_intestine(4)|lung(10)|urinary_tract(1)	20						CCAGATTTGCTGAAATTATTG	0.468													t|||	3828	0.764377	0.8396	0.7637	5008	,	,		19653	0.9018		0.659	False		,,,				2504	0.6299				p.A216A		Atlas-SNP	.											.	LAP3	50	.	0			c.T648C						PASS	.	C		3622,784	752.5+/-412.3	1491,640,72	103.0	103.0	103.0		648	-9.5	0.0	4	dbSNP_107	103	5452,3148	655.8+/-401.3	1712,2028,560	no	coding-synonymous	LAP3	NM_015907.2		3203,2668,632	CC,CT,TT		36.6047,17.7939,30.2322		216/520	17586703	9074,3932	2203	4300	6503	SO:0001819	synonymous_variant	51056	exon6			ATTTGCTGAAATT	AF061738	CCDS3422.1	4p15.33	2012-07-25	2003-09-12		ENSG00000002549	ENSG00000002549	3.4.11.1		18449	protein-coding gene	gene with protein product		170250	"""peptidase S"""	PEPS		6350155, 689684	Standard	NM_015907		Approved	LAPEP, LAP	uc003gph.1	P28838	OTTHUMG00000048214	ENST00000226299.4:c.648T>C	4.37:g.17586703T>C		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	99	7	0.0707071	NM_015907	B3KMQ3|Q6IAM6|Q6P0L6|Q9UQE3	Silent	SNP	ENST00000226299.4	37	CCDS3422.1																																																																																			T|0.266;C|0.734	0.734	strong		0.468	LAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250365.1		
CDH23	64072	hgsc.bcm.edu	37	10	73466709	73466709	+	Silent	SNP	T	T	C	rs10823829	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr10:73466709T>C	ENST00000224721.6	+	25	3029	c.3024T>C	c.(3022-3024)tcT>tcC	p.S1008S	CDH23_ENST00000299366.7_Silent_p.S1048S	NM_022124.5	NP_071407.4	Q9H251	CAD23_HUMAN	cadherin-related 23	1003	Cadherin 10. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium ion transport (GO:0006816)|calcium-dependent cell-cell adhesion (GO:0016339)|cytosolic calcium ion homeostasis (GO:0051480)|equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|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)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(6)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(27)|lung(49)|ovary(3)|pancreas(1)|prostate(7)|stomach(7)|upper_aerodigestive_tract(3)	133						ACAATGTGTCTGTGTCCGAGG	0.637													C|||	1039	0.207468	0.4062	0.1513	5008	,	,		19342	0.2698		0.0348	False		,,,				2504	0.092				p.S1003S		Atlas-SNP	.											.	CDH23	365	.	0			c.T3009C						PASS	.	C	,,	1436,2890		225,986,952	43.0	54.0	51.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	3009,3009,3009	-4.1	0.7	10	dbSNP_120	51	277,8211		5,267,3972	no	coding-synonymous,coding-synonymous,coding-synonymous	CDH23	NM_001171930.1,NM_001171931.1,NM_022124.5	,,	230,1253,4924	CC,CT,TT		3.2634,33.1946,13.3682	,,	1003/1382,1003/1062,1003/3355	73466709	1713,11101	2163	4244	6407	SO:0001819	synonymous_variant	64072	exon25			TGTGTCTGTGTCC	AY010111	CCDS53540.1, CCDS73146.1	10q22.1	2014-08-08	2010-01-25		ENSG00000107736	ENSG00000107736		"""Cadherins / Cadherin-related"""	13733	protein-coding gene	gene with protein product	"""cadherin-related family member 23"""	605516	"""cadherin related 23"", ""cadherin-like 23"""	DFNB12, USH1D		11090341	Standard	NM_022124		Approved	CDHR23	uc001jrx.4	Q9H251	OTTHUMG00000019347	ENST00000224721.6:c.3024T>C	10.37:g.73466709T>C		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	120	8	0.0666667	NM_022124	C4IXS9|F6U049|Q5QGS1|Q5QGS2|Q5QGS5|Q5QGS6|Q5XKN2|Q6UWW1|Q96JL3|Q9H4K9	Silent	SNP	ENST00000224721.6	37																																																																																				T|0.793;C|0.207	0.207	strong		0.637	CDH23-001	PUTATIVE	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051227.4	NM_052836	
NAV2	89797	hgsc.bcm.edu	37	11	20071386	20071386	+	Missense_Mutation	SNP	C	C	G	rs76731633	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr11:20071386C>G	ENST00000396087.3	+	17	4543	c.4444C>G	c.(4444-4446)Ctc>Gtc	p.L1482V	NAV2_ENST00000540292.1_Missense_Mutation_p.L1413V|NAV2_ENST00000311043.8_Intron|NAV2_ENST00000533917.1_Intron|NAV2_ENST00000349880.4_Missense_Mutation_p.L1459V|NAV2_ENST00000360655.4_Missense_Mutation_p.L1395V|NAV2_ENST00000527559.2_Missense_Mutation_p.L1411V|NAV2_ENST00000396085.1_Missense_Mutation_p.L1459V|NAV2-AS2_ENST00000533767.1_RNA	NM_001244963.1	NP_001231892.1	Q8IVL1	NAV2_HUMAN	neuron navigator 2	1482	Ser-rich.				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						TTCTAGCCCTCTCTCTTCCCC	0.493													C|||	3	0.000599042	0.0	0.0	5008	,	,		19931	0.003		0.0	False		,,,				2504	0.0				p.L1482V		Atlas-SNP	.											.	NAV2	255	.	0			c.C4444G						PASS	.						150.0	144.0	146.0					11																	20071386		2203	4300	6503	SO:0001583	missense	89797	exon17			AGCCCTCTCTCTT	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.4444C>G	11.37:g.20071386C>G	ENSP00000379396:p.Leu1482Val	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	96	4	0.0416667	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	0	0.0	0	0.0	2	0.0034965034965034965	0	0.0	C	12.83	2.055579	0.36277	.	.	ENSG00000166833	ENST00000360655;ENST00000396085;ENST00000349880;ENST00000396087;ENST00000527559;ENST00000540292	T;T;T;T;T;T	0.28666	1.61;1.71;1.71;1.69;1.6;1.6	5.82	5.82	0.92795	.	0.000000	0.53938	D	0.000057	T	0.26048	0.0635	L	0.29908	0.895	0.80722	D	1	B;B	0.28082	0.2;0.11	B;B	0.28465	0.09;0.033	T	0.03493	-1.1031	9	.	.	.	.	18.2759	0.90083	0.0:1.0:0.0:0.0	.	1459;1395	Q8IVL1-3;Q8IVL1-4	.;.	V	1395;1459;1459;1482;1411;1413	ENSP00000353871:L1395V;ENSP00000379394:L1459V;ENSP00000309577:L1459V;ENSP00000379396:L1482V;ENSP00000435395:L1411V;ENSP00000443489:L1413V	.	L	+	1	0	NAV2	20027962	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.818000	0.86416	2.767000	0.95098	0.655000	0.94253	CTC	C|0.998;G|0.002	0.002	strong		0.493	NAV2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324112.1	NM_145117	
KIF13A	63971	hgsc.bcm.edu	37	6	17764996	17764996	+	Missense_Mutation	SNP	C	C	T	rs184686655	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr6:17764996C>T	ENST00000259711.6	-	39	4868	c.4763G>A	c.(4762-4764)cGt>cAt	p.R1588H	KIF13A_ENST00000378843.2_Missense_Mutation_p.R1540H|KIF13A_ENST00000378816.5_Missense_Mutation_p.R1553H|KIF13A_ENST00000378826.2_Missense_Mutation_p.R1553H|KIF13A_ENST00000378814.5_Missense_Mutation_p.R1540H	NM_022113.5	NP_071396.4	Q9H1H9	KI13A_HUMAN	kinesin family member 13A	1588					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)			GGTAGGGCTACGGGACACTTC	0.502													C|||	2	0.000399361	0.0008	0.0014	5008	,	,		19335	0.0		0.0	False		,,,				2504	0.0				p.R1588H		Atlas-SNP	.											.	KIF13A	276	.	0			c.G4763A						PASS	.	C	HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG	1,4005		0,1,2002	84.0	83.0	84.0		4658,4619,4619,4763	6.1	1.0	6		84	3,8327		0,3,4162	yes	missense,missense,missense,missense	KIF13A	NM_001105566.2,NM_001105567.2,NM_001105568.2,NM_022113.5	29,29,29,29	0,4,6164	TT,TC,CC		0.036,0.025,0.0324	probably-damaging,probably-damaging,probably-damaging,probably-damaging	1553/1771,1540/1758,1540/1750,1588/1806	17764996	4,12332	2003	4165	6168	SO:0001583	missense	63971	exon39			GGGCTACGGGACA	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.4763G>A	6.37:g.17764996C>T	ENSP00000259711:p.Arg1588His	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	86	28	0.325581	NM_022113	A0JP21|A0JP22|F2Z382|Q5THQ2|Q5THQ3|Q9H193|Q9H194|Q9H1H8	Missense_Mutation	SNP	ENST00000259711.6	37	CCDS47381.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	C	31	5.074668	0.94000	2.5E-4	3.6E-4	ENSG00000137177	ENST00000378814;ENST00000502297;ENST00000259711;ENST00000378826;ENST00000378843;ENST00000378816	T;T;T;T;T;T	0.51071	0.72;0.72;0.72;0.72;0.72;0.72	6.07	6.07	0.98685	.	0.275476	0.29280	N	0.012608	T	0.53126	0.1777	L	0.34521	1.04	0.58432	D	0.999994	D;D;D;D	0.89917	1.0;0.999;1.0;0.999	D;P;D;P	0.81914	0.995;0.897;0.951;0.897	T	0.41431	-0.9509	10	0.36615	T	0.2	.	20.6525	0.99598	0.0:1.0:0.0:0.0	.	1540;1553;1588;1540	Q9H1H9-4;Q9H1H9-2;Q9H1H9;Q9H1H9-3	.;.;KI13A_HUMAN;.	H	1540;592;1588;1553;1540;1553	ENSP00000368091:R1540H;ENSP00000425616:R592H;ENSP00000259711:R1588H;ENSP00000368103:R1553H;ENSP00000368120:R1540H;ENSP00000368093:R1553H	ENSP00000259711:R1588H	R	-	2	0	KIF13A	17872975	1.000000	0.71417	0.992000	0.48379	0.998000	0.95712	7.469000	0.80959	2.890000	0.99128	0.585000	0.79938	CGT	C|1.000;T|0.000	0.000	strong		0.502	KIF13A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039954.4		
PM20D2	135293	hgsc.bcm.edu	37	6	89868128	89868128	+	Missense_Mutation	SNP	A	A	G	rs10944433	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr6:89868128A>G	ENST00000275072.4	+	5	1092	c.997A>G	c.(997-999)Aag>Gag	p.K333E		NM_001010853.1	NP_001010853.1	Q8IYS1	P20D2_HUMAN	peptidase M20 domain containing 2	333			K -> E (in dbSNP:rs10944433).			extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	hydrolase activity (GO:0016787)			breast(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(3)|lung(2)|skin(1)	12		all_cancers(76;9.47e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.45e-10)|all_hematologic(105;7.74e-07)|all_epithelial(107;0.000114)		BRCA - Breast invasive adenocarcinoma(108;0.00813)		AAATGGAAGAAAGCTAGGAAT	0.328													A|||	109	0.0217652	0.0106	0.0086	5008	,	,		16585	0.0437		0.0	False		,,,				2504	0.046				p.K333E		Atlas-SNP	.											PM20D2,NS,carcinoma,-1,1	PM20D2	30	1	0			c.A997G						scavenged	.	A	GLU/LYS	43,4363	46.0+/-80.4	0,43,2160	102.0	112.0	109.0		997	5.3	0.9	6	dbSNP_120	109	5,8593	4.3+/-15.6	0,5,4294	yes	missense	PM20D2	NM_001010853.1	56	0,48,6454	GG,GA,AA		0.0582,0.9759,0.3691	benign	333/437	89868128	48,12956	2203	4299	6502	SO:0001583	missense	135293	exon5			GGAAGAAAGCTAG	BC035036	CCDS34499.1	6q15	2014-07-14	2007-11-14	2007-11-14	ENSG00000146281	ENSG00000146281			21408	protein-coding gene	gene with protein product	"""&#946;-alanyl-lysine dipeptidase"""	615913	"""aminoacylase 1-like 2"""	ACY1L2		24891507	Standard	NM_001010853		Approved	bA63L7.3	uc003pmz.4	Q8IYS1	OTTHUMG00000015193	ENST00000275072.4:c.997A>G	6.37:g.89868128A>G	ENSP00000275072:p.Lys333Glu	Somatic	313	2	0.00638978		WXS	Illumina HiSeq	Phase_I	219	8	0.0365297	NM_001010853	B4DYJ2|Q5T7J9|Q6MZV2|Q86XD9	Missense_Mutation	SNP	ENST00000275072.4	37	CCDS34499.1	37	0.01694139194139194	5	0.01016260162601626	4	0.011049723756906077	28	0.04895104895104895	0	0.0	A	6.550	0.469673	0.12461	0.009759	5.82E-4	ENSG00000146281	ENST00000275072	T	0.38887	1.11	5.32	5.32	0.75619	.	0.159328	0.56097	D	0.000024	T	0.10895	0.0266	N	0.12920	0.275	0.36178	D	0.84924	B	0.23806	0.091	B	0.25987	0.065	T	0.05178	-1.0901	10	0.02654	T	1	-14.5741	15.309	0.74016	1.0:0.0:0.0:0.0	rs10944433;rs52835700;rs10944433	333	Q8IYS1	P20D2_HUMAN	E	333	ENSP00000275072:K333E	ENSP00000275072:K333E	K	+	1	0	PM20D2	89924847	0.992000	0.36948	0.945000	0.38365	0.394000	0.30568	2.606000	0.46291	2.016000	0.59253	0.477000	0.44152	AAG	A|0.990;G|0.010	0.010	strong		0.328	PM20D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041477.1	NM_001010853	
NR4A3	8013	hgsc.bcm.edu	37	9	102595685	102595685	+	Silent	SNP	C	C	T	rs10988904	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr9:102595685C>T	ENST00000395097.2	+	5	1932	c.1203C>T	c.(1201-1203)gcC>gcT	p.A401A	NR4A3_ENST00000330847.1_Silent_p.A412A|NR4A3_ENST00000338488.4_Silent_p.A401A	NM_006981.3|NM_173200.2	NP_008912.2|NP_775292.1	Q92570	NR4A3_HUMAN	nuclear receptor subfamily 4, group A, member 3	401					gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|steroid hormone receptor activity (GO:0003707)|thyroid hormone receptor activity (GO:0004887)|zinc ion binding (GO:0008270)		TCF12/NR4A3(2)|TAF15/NR4A3(33)|EWSR1/NR4A3(146)|TFG/NR4A3(2)				Acute lymphoblastic leukemia(62;0.0559)|all_hematologic(171;0.189)				TGATGAATGCCCTTGTCCGAG	0.453			T	EWSR1	extraskeletal myxoid chondrosarcoma								C|||	1455	0.290535	0.4191	0.2695	5008	,	,		19484	0.1687		0.3857	False		,,,				2504	0.1595				p.A412A		Atlas-SNP	.		Dom	yes		9	9q22	8013	"""nuclear receptor subfamily 4, group A, member 3 (NOR1)"""		M	.	NR4A3	80	.	0			c.C1236T						PASS	.	C	,,	1679,2727	508.9+/-367.1	319,1041,843	201.0	182.0	189.0		1203,1203,1236	4.8	1.0	9	dbSNP_120	189	3124,5476	475.6+/-369.2	575,1974,1751	no	coding-synonymous,coding-synonymous,coding-synonymous	NR4A3	NM_006981.3,NM_173199.2,NM_173200.2	,,	894,3015,2594	TT,TC,CC		36.3256,38.1071,36.9291	,,	401/627,401/444,412/638	102595685	4803,8203	2203	4300	6503	SO:0001819	synonymous_variant	8013	exon6			GAATGCCCTTGTC	U12767	CCDS6742.1, CCDS6743.1, CCDS6744.1	9q22	2013-01-16			ENSG00000119508	ENSG00000119508		"""Nuclear hormone receptors"""	7982	protein-coding gene	gene with protein product		600542				8614405	Standard	NM_006981		Approved	CSMF, CHN, NOR1, MINOR	uc004baf.1	Q92570	OTTHUMG00000021030	ENST00000395097.2:c.1203C>T	9.37:g.102595685C>T		Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	171	7	0.0409357	NM_173200	A2A3I7|Q12935|Q14979|Q16420|Q4VXA8|Q4VXA9|Q9UEK2|Q9UEK3	Silent	SNP	ENST00000395097.2	37	CCDS6743.1																																																																																			C|0.649;T|0.351	0.351	strong		0.453	NR4A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055482.1		
SLC15A2	6565	hgsc.bcm.edu	37	3	121647286	121647286	+	Missense_Mutation	SNP	C	C	T	rs1143671	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr3:121647286C>T	ENST00000489711.1	+	15	1613	c.1225C>T	c.(1225-1227)Cca>Tca	p.P409S	SLC15A2_ENST00000465060.1_3'UTR|SLC15A2_ENST00000295605.2_Missense_Mutation_p.P378S	NM_021082.3	NP_066568.3	Q16348	S15A2_HUMAN	solute carrier family 15 (oligopeptide transporter), member 2	409			P -> S (in dbSNP:rs1143671).		drug transport (GO:0015893)|ion transport (GO:0006811)|protein transport (GO:0015031)|proton transport (GO:0015992)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	antibiotic transporter activity (GO:0042895)|dipeptide transporter activity (GO:0042936)|high-affinity oligopeptide transporter activity (GO:0015334)|peptide:proton symporter activity (GO:0015333)			NS(1)|endometrium(1)|kidney(4)|large_intestine(5)|lung(17)|skin(6)|upper_aerodigestive_tract(2)	36				GBM - Glioblastoma multiforme(114;0.0967)	Aminolevulinic acid(DB00855)|Amoxicillin(DB01060)|Ampicillin(DB00415)|Azidocillin(DB08795)|Benazepril(DB00542)|Benzylpenicillin(DB01053)|Cefaclor(DB00833)|Cefadroxil(DB01140)|Cefalotin(DB00456)|Cefdinir(DB00535)|Cefepime(DB01413)|Cefixime(DB00671)|Cefmetazole(DB00274)|Cefotaxime(DB00493)|Cefradine(DB01333)|Ceftazidime(DB00438)|Ceftibuten(DB01415)|Ceftriaxone(DB01212)|Cefuroxime(DB01112)|Cephalexin(DB00567)|Chlorpropamide(DB00672)|Cilazapril(DB01340)|Cloxacillin(DB01147)|Cyclacillin(DB01000)|Dicloxacillin(DB00485)|Fosinopril(DB00492)|Glyburide(DB01016)|Moexipril(DB00691)|Nateglinide(DB00731)|Oxacillin(DB00713)|Perindopril(DB00790)|Quinapril(DB00881)|Ramipril(DB00178)|Spirapril(DB01348)|Tolbutamide(DB01124)|Trandolapril(DB00519)|Tranexamic Acid(DB00302)|Valaciclovir(DB00577)|Valganciclovir(DB01610)	CCCAGCCCAGCCAGGTCCCCA	0.443													T|||	2263	0.451877	0.4834	0.2939	5008	,	,		19560	0.6984		0.4235	False		,,,				2504	0.2965				p.P409S		Atlas-SNP	.											.	SLC15A2	92	.	0			c.C1225T						PASS	.	T	SER/PRO,SER/PRO	2150,2256	595.1+/-388.4	532,1086,585	161.0	165.0	163.0		1132,1225	-0.5	0.0	3	dbSNP_86	163	3905,4695	606.1+/-395.0	880,2145,1275	yes	missense,missense	SLC15A2	NM_001145998.1,NM_021082.3	74,74	1412,3231,1860	TT,TC,CC		45.407,48.7971,46.5554	possibly-damaging,possibly-damaging	378/699,409/730	121647286	6055,6951	2203	4300	6503	SO:0001583	missense	6565	exon15			GCCCAGCCAGGTC	BC044572	CCDS3007.1, CCDS54631.1	3q21.1	2013-07-18	2013-07-18		ENSG00000163406	ENSG00000163406		"""Solute carriers"""	10921	protein-coding gene	gene with protein product		602339	"""solute carrier family 15 (H+/peptide transporter), member 2"""			7756356	Standard	NM_021082		Approved	PEPT2	uc003eep.2	Q16348	OTTHUMG00000159423	ENST00000489711.1:c.1225C>T	3.37:g.121647286C>T	ENSP00000417085:p.Pro409Ser	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	56	6	0.107143	NM_021082	A8K1A5|B4E2A7	Missense_Mutation	SNP	ENST00000489711.1	37	CCDS3007.1	1071	0.49038461538461536	227	0.4613821138211382	100	0.27624309392265195	427	0.7465034965034965	317	0.4182058047493404	T	10.32	1.317079	0.23908	0.487971	0.45407	ENSG00000163406	ENST00000489711;ENST00000542599;ENST00000295605	T;T	0.05447	3.44;3.44	5.61	-0.531	0.11894	.	0.512979	0.23208	N	0.050705	T	0.00012	0.0000	M	0.86097	2.795	0.58432	P	2.9999999999752447E-6	P;D	0.53462	0.809;0.96	P;P	0.59595	0.517;0.86	T	0.41752	-0.9491	9	0.59425	D	0.04	0.0419	2.425	0.04457	0.2192:0.406:0.2314:0.1434	rs1143671;rs1316300;rs3749457;rs52819015;rs59056692;rs1143671	378;409	B4E2A7;Q16348	.;S15A2_HUMAN	S	409;371;378	ENSP00000417085:P409S;ENSP00000295605:P378S	ENSP00000295605:P378S	P	+	1	0	SLC15A2	123129976	0.313000	0.24554	0.004000	0.12327	0.084000	0.17831	-0.176000	0.09811	-0.540000	0.06265	-0.743000	0.03520	CCA	C|0.523;T|0.477	0.477	strong		0.443	SLC15A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355239.1	NM_021082	
PLCH1	23007	hgsc.bcm.edu	37	3	155218568	155218568	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr3:155218568G>A	ENST00000340059.7	-	13	1683	c.1684C>T	c.(1684-1686)Cgg>Tgg	p.R562W	PLCH1_ENST00000460012.1_Missense_Mutation_p.R544W|PLCH1_ENST00000414191.1_Missense_Mutation_p.R544W|PLCH1_ENST00000447496.2_Missense_Mutation_p.R562W|PLCH1_ENST00000334686.6_Missense_Mutation_p.R544W|PLCH1_ENST00000494598.1_Missense_Mutation_p.R562W	NM_001130960.1	NP_001124432.1	Q4KWH8	PLCH1_HUMAN	phospholipase C, eta 1	562					inositol phosphate metabolic process (GO:0043647)|lipid catabolic process (GO:0016042)|phosphatidylinositol-mediated signaling (GO:0048015)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calcium-dependent phospholipase C activity (GO:0050429)|phosphatidylinositol phospholipase C activity (GO:0004435)|signal transducer activity (GO:0004871)			NS(3)|breast(3)|endometrium(9)|kidney(4)|large_intestine(20)|lung(45)|ovary(2)|prostate(5)|skin(8)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(4)	107			Lung(72;0.11)|LUSC - Lung squamous cell carcinoma(72;0.114)			GATTTAGACCGTGATTTTGTA	0.393																																					p.R562W		Atlas-SNP	.											.	PLCH1	406	.	0			c.C1684T						PASS	.						194.0	176.0	182.0					3																	155218568		2203	4300	6503	SO:0001583	missense	23007	exon13			TAGACCGTGATTT	AB028992	CCDS33881.1, CCDS46939.1, CCDS46940.1	3q25	2013-01-10	2006-03-16	2006-03-16	ENSG00000114805	ENSG00000114805	3.1.4.11	"""EF-hand domain containing"""	29185	protein-coding gene	gene with protein product		612835	"""phospholipase C-like 3"""	PLCL3		15702972	Standard	NM_014996		Approved	KIAA1069, MGC117152, DKFZp434C1372, PLCeta1	uc021xge.1	Q4KWH8	OTTHUMG00000158477	ENST00000340059.7:c.1684C>T	3.37:g.155218568G>A	ENSP00000345988:p.Arg562Trp	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	63	7	0.111111	NM_001130960	Q29RV9|Q4KWH9|Q68CN0|Q86XK4|Q9H9U2|Q9UPT3	Missense_Mutation	SNP	ENST00000340059.7	37	CCDS46939.1	.	.	.	.	.	.	.	.	.	.	G	18.13	3.554572	0.65425	.	.	ENSG00000114805	ENST00000494598;ENST00000460012;ENST00000447496;ENST00000340059;ENST00000334686;ENST00000414191	T;T;T;T;T;T	0.53423	0.62;0.62;0.62;0.62;0.62;0.62	5.81	3.84	0.44239	PLC-like phosphodiesterase, TIM beta/alpha-barrel domain (1);	0.619336	0.16832	N	0.197725	T	0.58119	0.2100	L	0.56769	1.78	0.41436	D	0.98789	D;D;D	0.69078	0.997;0.995;0.995	P;P;P	0.60473	0.875;0.753;0.663	T	0.59204	-0.7498	10	0.66056	D	0.02	.	9.7551	0.40498	0.0:0.1019:0.557:0.3411	.	544;562;562	Q4KWH8-2;Q4KWH8;Q4KWH8-3	.;PLCH1_HUMAN;.	W	562;544;562;562;544;544	ENSP00000419100:R562W;ENSP00000417502:R544W;ENSP00000402759:R562W;ENSP00000345988:R562W;ENSP00000335469:R544W;ENSP00000412977:R544W	ENSP00000335469:R544W	R	-	1	2	PLCH1	156701262	0.987000	0.35691	0.993000	0.49108	0.996000	0.88848	1.413000	0.34725	2.736000	0.93811	0.655000	0.94253	CGG	.	.	none		0.393	PLCH1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000351125.1	NM_014996	
HBS1L	10767	hgsc.bcm.edu	37	6	135287533	135287533	+	Silent	SNP	A	A	G	rs13064	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr6:135287533A>G	ENST00000367837.5	-	17	2183	c.1977T>C	c.(1975-1977)ttT>ttC	p.F659F	HBS1L_ENST00000367826.2_Silent_p.F617F|HBS1L_ENST00000415177.2_Silent_p.F594F|HBS1L_ENST00000527578.1_Silent_p.F495F|HBS1L_ENST00000367824.4_Silent_p.F495F|HBS1L_ENST00000445176.2_Silent_p.F383F	NM_001145158.1|NM_006620.3	NP_001138630.1|NP_006611.1	Q9Y450	HBS1L_HUMAN	HBS1-like translational GTPase	659					signal transduction (GO:0007165)|translation (GO:0006412)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|translation elongation factor activity (GO:0003746)			NS(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	20	Colorectal(23;0.221)			OV - Ovarian serous cystadenocarcinoma(155;0.0046)|GBM - Glioblastoma multiforme(68;0.00702)		CCAGCTCTTTAAAGTCTTTAT	0.368													A|||	1299	0.259385	0.1906	0.2378	5008	,	,		16977	0.245		0.3549	False		,,,				2504	0.2843				p.F659F		Atlas-SNP	.											.	HBS1L	75	.	0			c.T1977C						PASS	.	A	,	1011,3395	376.8+/-322.2	113,785,1305	143.0	136.0	138.0		1851,1977	-9.0	0.4	6	dbSNP_52	138	3205,5395	484.5+/-371.4	595,2015,1690	no	coding-synonymous,coding-synonymous	HBS1L	NM_001145158.1,NM_006620.3	,	708,2800,2995	GG,GA,AA		37.2674,22.946,32.4158	,	617/643,659/685	135287533	4216,8790	2203	4300	6503	SO:0001819	synonymous_variant	10767	exon17			CTCTTTAAAGTCT	U87791	CCDS5173.1, CCDS47479.1, CCDS47480.1	6q23.3	2014-04-30	2014-04-30		ENSG00000112339	ENSG00000112339			4834	protein-coding gene	gene with protein product	"""eRF3 family member"""	612450	"""HBS1 (S. cerevisiae)-like"", ""HBS1-like (S. cerevisiae)"""			9872408, 23667253	Standard	NM_006620		Approved	ERFS, HBS1, HSPC276, KIAA1038, DKFZp434g247, EF-1a, eRF3c	uc003qez.2	Q9Y450	OTTHUMG00000015626	ENST00000367837.5:c.1977T>C	6.37:g.135287533A>G		Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	98	6	0.0612245	NM_006620	B7Z365|Q4VX89|Q4VX90|Q5T7G3|Q8NDW9|Q9UPW3	Silent	SNP	ENST00000367837.5	37	CCDS5173.1																																																																																			A|0.692;G|0.308	0.308	strong		0.368	HBS1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042339.2		
PROSER1	80209	hgsc.bcm.edu	37	13	39603498	39603498	+	Silent	SNP	G	G	A	rs61737582	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr13:39603498G>A	ENST00000352251.3	-	4	1028	c.195C>T	c.(193-195)gtC>gtT	p.V65V	PROSER1_ENST00000350125.3_Silent_p.V43V	NM_025138.4	NP_079414.3	Q86XN7	PRSR1_HUMAN	proline and serine rich 1	65																	CTGTTGGCTGGACAGCCACCA	0.318													G|||	457	0.091254	0.0855	0.1095	5008	,	,		15384	0.0903		0.0586	False		,,,				2504	0.1207				p.V65V		Atlas-SNP	.											C13orf23,NS,carcinoma,-2,1	.	.	1	0			c.C195T						scavenged	.	G	,	214,3394		4,206,1594	72.0	71.0	71.0		195,129	-0.0	1.0	13	dbSNP_129	71	525,7617		16,493,3562	no	coding-synonymous,coding-synonymous	PROSER1	NM_025138.3,NM_170719.2	,	20,699,5156	AA,AG,GG		6.448,5.9313,6.2894	,	65/945,43/923	39603498	739,11011	1804	4071	5875	SO:0001819	synonymous_variant	80209	exon4			TGGCTGGACAGCC	AK022723	CCDS9368.2	13q13.2	2011-08-09	2011-08-09	2011-08-09	ENSG00000120685	ENSG00000120685			20291	protein-coding gene	gene with protein product			"""chromosome 13 open reading frame 23"""	C13orf23			Standard	NM_025138		Approved	bA50D16.2, FLJ12661	uc001uwy.4	Q86XN7	OTTHUMG00000016764	ENST00000352251.3:c.195C>T	13.37:g.39603498G>A		Somatic	307	0	0		WXS	Illumina HiSeq	Phase_I	275	9	0.0327273	NM_025138	A6NJ97|Q6P2S2|Q7Z3X5|Q8N3D2|Q8N3P1|Q9H9M1	Silent	SNP	ENST00000352251.3	37	CCDS9368.2																																																																																			G|0.921;A|0.079	0.079	strong		0.318	PROSER1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044607.5	NM_025138	
XIRP2	129446	hgsc.bcm.edu	37	2	168107491	168107491	+	Missense_Mutation	SNP	A	A	G	rs3749004	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr2:168107491A>G	ENST00000409195.1	+	9	9678	c.9589A>G	c.(9589-9591)Atc>Gtc	p.I3197V	XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000409273.1_Missense_Mutation_p.I2975V|XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000409728.1_Intron|XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000295237.9_Missense_Mutation_p.I3197V|XIRP2_ENST00000409756.2_Intron	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	3022					actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)				NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						CAAAGGGGCCATCCCATGTCC	0.473													A|||	992	0.198083	0.326	0.1326	5008	,	,		18868	0.12		0.1233	False		,,,				2504	0.229				p.I3197V		Atlas-SNP	.											.	XIRP2	914	.	0			c.A9589G						PASS	.	A	,,,VAL/ILE,VAL/ILE	1086,2824		160,766,1029	81.0	84.0	83.0		,,,9589,8923	-4.1	0.0	2	dbSNP_107	83	924,7380		56,812,3284	yes	intron,intron,intron,missense,missense	XIRP2	NM_001079810.3,NM_001199143.1,NM_001199145.1,NM_152381.5,NM_001199144.1	,,,29,29	216,1578,4313	GG,GA,AA		11.1272,27.7749,16.4565	,,,benign,benign	,,,3197/3550,2975/3328	168107491	2010,10204	1955	4152	6107	SO:0001583	missense	129446	exon9			GGGGCCATCCCAT	AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"""myomaxin"""	609778	"""cardiomyopathy associated 3"""	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409195.1:c.9589A>G	2.37:g.168107491A>G	ENSP00000386840:p.Ile3197Val	Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	130	6	0.0461538	NM_152381	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Missense_Mutation	SNP	ENST00000409195.1	37	CCDS42769.1	386	0.17673992673992675	172	0.34959349593495936	47	0.1298342541436464	72	0.1258741258741259	95	0.12532981530343007	A	0.111	-1.138744	0.01742	0.277749	0.111272	ENSG00000163092	ENST00000409195;ENST00000295237;ENST00000409273;ENST00000413534	T;T;T	0.02631	4.22;4.22;4.22	5.45	-4.1	0.03940	.	1.015070	0.07871	N	0.967851	T	0.00012	0.0000	N	0.25144	0.715	0.80722	P	0.0	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.09377	0.002;0.004;0.003	T	0.46345	-0.9198	9	0.19590	T	0.45	-0.4673	4.6634	0.12653	0.6565:0.0998:0.146:0.0977	rs3749004;rs52810850;rs58049014;rs3749004	3022;3022;2975	A4UGR9;A4UGR9-3;A4UGR9-2	XIRP2_HUMAN;.;.	V	3197;3197;2975;611	ENSP00000386840:I3197V;ENSP00000295237:I3197V;ENSP00000387255:I2975V	ENSP00000295237:I3197V	I	+	1	0	XIRP2	167815737	0.000000	0.05858	0.001000	0.08648	0.776000	0.43924	0.291000	0.18994	-0.431000	0.07307	0.377000	0.23210	ATC	A|0.817;G|0.183	0.183	strong		0.473	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381	
C8orf48	157773	hgsc.bcm.edu	37	8	13424866	13424866	+	Silent	SNP	G	G	C	rs75484711	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr8:13424866G>C	ENST00000297324.4	+	1	515	c.366G>C	c.(364-366)ctG>ctC	p.L122L	RP11-145O15.3_ENST00000529018.1_RNA	NM_001007090.2	NP_001007091	Q96LL4	CH048_HUMAN	chromosome 8 open reading frame 48	122										NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|prostate(1)	5						TGAATGCCCTGCAGTCTTATT	0.423													G|||	154	0.0307508	0.0008	0.0245	5008	,	,		17973	0.126		0.0	False		,,,				2504	0.0092				p.L122L		Atlas-SNP	.											.	C8orf48	18	.	0			c.G366C						PASS	.						64.0	56.0	58.0					8																	13424866		692	1591	2283	SO:0001819	synonymous_variant	157773	exon1			TGCCCTGCAGTCT	AK058131	CCDS47809.1	8p22	2012-04-13			ENSG00000164743	ENSG00000164743			26345	protein-coding gene	gene with protein product						12477932	Standard	NM_001007090		Approved	FLJ25402	uc003wwp.3	Q96LL4	OTTHUMG00000165482	ENST00000297324.4:c.366G>C	8.37:g.13424866G>C		Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	158	9	0.056962	NM_001007090	Q96LJ9	Silent	SNP	ENST00000297324.4	37	CCDS47809.1																																																																																			G|0.960;C|0.040	0.040	strong		0.423	C8orf48-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384400.1	NM_001007090	
NCKAP5	344148	hgsc.bcm.edu	37	2	133542014	133542014	+	Silent	SNP	T	T	C	rs12616282	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr2:133542014T>C	ENST00000409261.1	-	14	2743	c.2370A>G	c.(2368-2370)gcA>gcG	p.A790A	NCKAP5_ENST00000405974.3_Intron|NCKAP5_ENST00000409213.1_Intron|NCKAP5_ENST00000317721.6_Silent_p.A790A|NCKAP5_ENST00000473859.1_5'Flank	NM_207363.2	NP_997246.2	O14513	NCKP5_HUMAN	NCK-associated protein 5	790										NS(4)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(29)|lung(51)|prostate(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	118						TGCCCATGGGTGCCGAAGACC	0.458													c|||	3548	0.708466	0.8328	0.67	5008	,	,		18099	0.8681		0.507	False		,,,				2504	0.6104				p.A790A		Atlas-SNP	.											.	NCKAP5	322	.	0			c.A2370G						PASS	.	C	,	3005,761		1211,583,89	133.0	134.0	134.0		2370,	-0.4	0.0	2	dbSNP_120	134	4348,3894		1139,2070,912	no	coding-synonymous,intron	NCKAP5	NM_207363.2,NM_207481.3	,	2350,2653,1001	CC,CT,TT		47.2458,20.2071,38.7658	,	790/1910,	133542014	7353,4655	1883	4121	6004	SO:0001819	synonymous_variant	344148	exon14			CATGGGTGCCGAA	AB005217	CCDS46417.1, CCDS46418.1	2q21.2	2010-02-17			ENSG00000176771	ENSG00000176771			29847	protein-coding gene	gene with protein product	"""Nck associated protein 5"", ""peripheral clock protein"""	608789				9344857	Standard	NM_207363		Approved	NAP5, ERIH1, ERIH2	uc002ttp.3	O14513	OTTHUMG00000153573	ENST00000409261.1:c.2370A>G	2.37:g.133542014T>C		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	106	5	0.0471698	NM_207363	B8ZZL0|Q29SS9|Q29ST0|Q2NL90|Q6ZVE2|Q8NAS3	Silent	SNP	ENST00000409261.1	37	CCDS46418.1																																																																																			T|0.335;C|0.665	0.665	strong		0.458	NCKAP5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331663.1	NM_207481	
PRG4	10216	hgsc.bcm.edu	37	1	186276961	186276961	+	Missense_Mutation	SNP	A	A	C	rs145338869	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr1:186276961A>C	ENST00000445192.2	+	7	2155	c.2110A>C	c.(2110-2112)Act>Cct	p.T704P	PRG4_ENST00000367484.3_Intron|PRG4_ENST00000367483.4_Missense_Mutation_p.T663P|PRG4_ENST00000367486.3_Missense_Mutation_p.T661P|PRG4_ENST00000367485.4_Missense_Mutation_p.T611P	NM_005807.3	NP_005798.2	Q92954	PRG4_HUMAN	proteoglycan 4	704	59 X 8 AA repeats of K-X-P-X-P-T-T-X.				cell proliferation (GO:0008283)|hematopoietic stem cell proliferation (GO:0071425)|immune response (GO:0006955)|negative regulation of interleukin-6 biosynthetic process (GO:0045409)|regulation of cell proliferation (GO:0042127)	extracellular space (GO:0005615)	polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(33)|prostate(7)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(1)	102						CCCTAAGGAGACTGCTCCAAC	0.597																																					p.T704P		Atlas-SNP	.											PRG4,NS,malignant_melanoma,0,1	PRG4	259	1	0			c.A2110C						PASS	.	A	PRO/THR,PRO/THR,PRO/THR,PRO/THR	15,4391		0,15,2188	137.0	152.0	147.0		2110,1708,1831,1987	-5.2	0.0	1	dbSNP_134	147	0,8600		0,0,4300	no	missense,missense,missense,missense	PRG4	NM_005807.3,NM_001127710.1,NM_001127709.1,NM_001127708.1	38,38,38,38	0,15,6488	CC,CA,AA		0.0,0.3404,0.1153	benign,benign,benign,benign	704/1405,570/1271,611/1312,663/1364	186276961	15,12991	2203	4300	6503	SO:0001583	missense	10216	exon7			AAGGAGACTGCTC	U70136	CCDS1369.1, CCDS44287.1, CCDS44288.1	1q25-q31	2008-07-18	2004-11-15		ENSG00000116690	ENSG00000116690			9364	protein-coding gene	gene with protein product	"""lubricin"", ""megakaryocyte stimulating factor"", ""articular superficial zone protein"", ""Jacobs camptodactyly-arthropathy-pericarditis syndrome"", ""camptodactyly, arthropathy, coxa vara, pericarditis syndrome"", ""bG174L6.2 (MSF: megakaryocyte stimulating factor )"""	604283	"""proteoglycan 4, (megakaryocyte stimulating factor, articular superficial zone protein, camptodactyly, arthropathy, coxa vara, pericarditis syndrome)"""	CACP		10545950, 9920774	Standard	NM_005807		Approved	JCAP, SZP, MSF, HAPO, bG174L6.2, FLJ32635	uc001gru.4	Q92954	OTTHUMG00000035574	ENST00000445192.2:c.2110A>C	1.37:g.186276961A>C	ENSP00000399679:p.Thr704Pro	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	113	6	0.0530973	NM_005807	Q6DNC4|Q6DNC5|Q6ZMZ5|Q9BX49	Missense_Mutation	SNP	ENST00000445192.2	37	CCDS1369.1	.	.	.	.	.	.	.	.	.	.	-	2.283	-0.364165	0.05103	0.003404	0.0	ENSG00000116690	ENST00000367486;ENST00000367482;ENST00000367483;ENST00000367485;ENST00000445192	T;T;T;T	0.05025	3.55;3.65;3.51;3.65	2.61	-5.23	0.02798	.	0.580677	0.14221	N	0.333433	T	0.01627	0.0052	N	0.02011	-0.69	0.09310	N	0.999999	B;B;B;B	0.06786	0.001;0.001;0.0;0.001	B;B;B;B	0.04013	0.001;0.001;0.0;0.001	T	0.39623	-0.9605	9	.	.	.	.	4.4579	0.11652	0.3649:0.3368:0.0:0.2984	.	570;611;704;663	Q92954-4;Q92954-3;Q92954;Q92954-2	.;.;PRG4_HUMAN;.	P	661;570;663;611;704	ENSP00000356456:T661P;ENSP00000356453:T663P;ENSP00000356455:T611P;ENSP00000399679:T704P	.	T	+	1	0	PRG4	184543584	0.005000	0.15991	0.000000	0.03702	0.060000	0.15804	0.317000	0.19487	-1.717000	0.01385	0.138000	0.15974	ACT	A|0.996;C|0.004	0.004	strong		0.597	PRG4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000086346.1	NM_005807	
SETD1B	23067	hgsc.bcm.edu	37	12	122247634	122247634	+	Silent	SNP	C	C	T			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr12:122247634C>T	ENST00000604567.1	+	6	851	c.783C>T	c.(781-783)tgC>tgT	p.C261C	SETD1B_ENST00000542440.1_Silent_p.C261C|SETD1B_ENST00000267197.5_Silent_p.C261C			Q9UPS6	SET1B_HUMAN	SET domain containing 1B	261					histone H3-K4 methylation (GO:0051568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)|Set1C/COMPASS complex (GO:0048188)	histone-lysine N-methyltransferase activity (GO:0018024)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			NS(1)|endometrium(6)|kidney(2)|prostate(2)	11						ATTCCAGCTGCCGCCTGGACA	0.647																																					p.C261C		Atlas-SNP	.											.	SETD1B	105	.	0			c.C783T						PASS	.						67.0	74.0	72.0					12																	122247634		692	1591	2283	SO:0001819	synonymous_variant	23067	exon5			CAGCTGCCGCCTG	AB028999	CCDS53838.1	12q24.31	2013-02-12			ENSG00000139718	ENSG00000139718		"""Chromatin-modifying enzymes / K-methyltransferases"", ""RNA binding motif (RRM) containing"""	29187	protein-coding gene	gene with protein product		611055				10470851, 17355966	Standard	NM_015048		Approved	KIAA1076, Set1B, KMT2G	uc001ubi.3	Q9UPS6	OTTHUMG00000169080	ENST00000604567.1:c.783C>T	12.37:g.122247634C>T		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	55	17	0.309091	NM_015048	F6MFW1	Silent	SNP	ENST00000604567.1	37																																																																																				.	.	none		0.647	SETD1B-002	PUTATIVE	non_canonical_U12|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000468264.1	XM_037523	
RAB11FIP2	22841	hgsc.bcm.edu	37	10	119774598	119774598	+	Missense_Mutation	SNP	T	T	A	rs58533443	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr10:119774598T>A	ENST00000355624.3	-	4	1728	c.1289A>T	c.(1288-1290)aAt>aTt	p.N430I	RP11-354M20.3_ENST00000595446.1_RNA|RAB11FIP2_ENST00000476207.1_5'UTR|RAB11FIP2_ENST00000369199.3_Missense_Mutation_p.N450I|RP11-354M20.3_ENST00000451610.2_RNA	NM_014904.2	NP_055719.1	Q7L804	RFIP2_HUMAN	RAB11 family interacting protein 2 (class I)	430					establishment of cell polarity (GO:0030010)|insulin secretion involved in cellular response to glucose stimulus (GO:0035773)|protein transport (GO:0015031)|regulated secretory pathway (GO:0045055)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cytoplasmic vesicle membrane (GO:0030659)|endosome (GO:0005768)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)			cervix(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(8)	19		Colorectal(252;0.235)		all cancers(201;0.0238)		GAGGTCTTCATTGCTTGTTGG	0.358													T|||	309	0.0617013	0.0431	0.072	5008	,	,		17272	0.1806		0.006	False		,,,				2504	0.0143				p.N430I		Atlas-SNP	.											.	RAB11FIP2	39	.	0			c.A1289T						PASS	.	T	ILE/ASN	188,4218	118.8+/-156.5	4,180,2019	90.0	85.0	87.0		1289	-3.6	1.0	10	dbSNP_129	87	42,8558	27.9+/-77.7	0,42,4258	yes	missense	RAB11FIP2	NM_014904.2	149	4,222,6277	AA,AT,TT		0.4884,4.2669,1.7684	benign	430/513	119774598	230,12776	2203	4300	6503	SO:0001583	missense	22841	exon4			TCTTCATTGCTTG	AY037299	CCDS7602.1	10q26.12	2004-07-22			ENSG00000107560	ENSG00000107560			29152	protein-coding gene	gene with protein product		608599				11994279, 10231032	Standard	NM_014904		Approved	KIAA0941, nRip11, Rab11-FIP2	uc001ldj.2	Q7L804	OTTHUMG00000019128	ENST00000355624.3:c.1289A>T	10.37:g.119774598T>A	ENSP00000347839:p.Asn430Ile	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	122	7	0.057377	NM_014904	A6NEI4|Q3I768|Q9Y2F0	Missense_Mutation	SNP	ENST00000355624.3	37	CCDS7602.1	149	0.06822344322344322	16	0.032520325203252036	18	0.049723756906077346	112	0.1958041958041958	3	0.00395778364116095	T	14.14	2.446920	0.43429	0.042669	0.004884	ENSG00000107560	ENST00000355624;ENST00000369199	T;T	0.63913	-0.07;-0.05	5.92	-3.59	0.04583	.	1.103000	0.06527	N	0.740675	T	0.00039	0.0001	N	0.14661	0.345	0.39854	P	0.02671100000000004	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.09143	-1.0688	9	0.49607	T	0.09	-0.1284	9.1794	0.37131	0.0:0.5334:0.2088:0.2578	rs58533443	450;430	Q3I768;Q7L804	.;RFIP2_HUMAN	I	430;450	ENSP00000347839:N430I;ENSP00000358200:N450I	ENSP00000347839:N430I	N	-	2	0	RAB11FIP2	119764588	0.296000	0.24398	0.979000	0.43373	0.990000	0.78478	-0.870000	0.04228	-0.270000	0.09285	0.528000	0.53228	AAT	T|0.967;A|0.033	0.033	strong		0.358	RAB11FIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050583.1	NM_014904	
TGFBR2	7048	hgsc.bcm.edu	37	3	30713842	30713842	+	Silent	SNP	C	C	T	rs2228048	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr3:30713842C>T	ENST00000295754.5	+	4	1549	c.1167C>T	c.(1165-1167)aaC>aaT	p.N389N	TGFBR2_ENST00000359013.4_Silent_p.N414N	NM_003242.5	NP_003233.4	P37173	TGFR2_HUMAN	transforming growth factor, beta receptor II (70/80kDa)	389	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of protein kinase activity (GO:0032147)|aging (GO:0007568)|apoptotic process (GO:0006915)|blood vessel development (GO:0001568)|brain development (GO:0007420)|bronchus morphogenesis (GO:0060434)|cartilage development (GO:0051216)|common-partner SMAD protein phosphorylation (GO:0007182)|digestive tract development (GO:0048565)|embryo implantation (GO:0007566)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic hemopoiesis (GO:0035162)|gastrulation (GO:0007369)|heart development (GO:0007507)|in utero embryonic development (GO:0001701)|lens development in camera-type eye (GO:0002088)|lens fiber cell apoptotic process (GO:1990086)|lung lobe morphogenesis (GO:0060463)|mammary gland morphogenesis (GO:0060443)|myeloid dendritic cell differentiation (GO:0043011)|negative regulation of cardiac muscle cell proliferation (GO:0060044)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|organ regeneration (GO:0031100)|palate development (GO:0060021)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|patterning of blood vessels (GO:0001569)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of angiogenesis (GO:0045766)|positive regulation of B cell tolerance induction (GO:0002663)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of NK T cell differentiation (GO:0051138)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of skeletal muscle tissue regeneration (GO:0043415)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of T cell tolerance induction (GO:0002666)|positive regulation of tolerance induction to self antigen (GO:0002651)|protein phosphorylation (GO:0006468)|receptor-mediated endocytosis (GO:0006898)|regulation of cell proliferation (GO:0042127)|response to cholesterol (GO:0070723)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to glucose (GO:0009749)|response to mechanical stimulus (GO:0009612)|response to nutrient (GO:0007584)|smoothened signaling pathway (GO:0007224)|trachea formation (GO:0060440)|transforming growth factor beta receptor signaling pathway (GO:0007179)|vasculogenesis (GO:0001570)|wound healing (GO:0042060)	caveola (GO:0005901)|cytosol (GO:0005829)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|transforming growth factor beta receptor homodimeric complex (GO:0070022)	ATP binding (GO:0005524)|glycosaminoglycan binding (GO:0005539)|metal ion binding (GO:0046872)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|SMAD binding (GO:0046332)|transforming growth factor beta binding (GO:0050431)|transforming growth factor beta receptor activity, type II (GO:0005026)|transforming growth factor beta-activated receptor activity (GO:0005024)|transmembrane receptor protein serine/threonine kinase activity (GO:0004675)|type I transforming growth factor beta receptor binding (GO:0034713)|type III transforming growth factor beta receptor binding (GO:0034714)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(15)|lung(10)|ovary(3)|pancreas(12)|skin(1)|stomach(5)|upper_aerodigestive_tract(2)	53						TCGTGAAGAACGACCTAACCT	0.557													C|||	518	0.103435	0.0431	0.0101	5008	,	,		21448	0.2986		0.0129	False		,,,				2504	0.1431				p.N414N		Atlas-SNP	.											.	TGFBR2	139	.	0			c.C1242T						PASS	.	C	,	143,4263	101.6+/-140.2	1,141,2061	305.0	268.0	281.0		1242,1167	-4.6	0.8	3	dbSNP_98	281	95,8505	52.7+/-113.3	0,95,4205	no	coding-synonymous,coding-synonymous	TGFBR2	NM_001024847.2,NM_003242.5	,	1,236,6266	TT,TC,CC		1.1047,3.2456,1.8299	,	414/593,389/568	30713842	238,12768	2203	4300	6503	SO:0001819	synonymous_variant	7048	exon5			GAAGAACGACCTA		CCDS2648.1, CCDS33727.1	3p22	2014-09-17	2002-08-29		ENSG00000163513	ENSG00000163513			11773	protein-coding gene	gene with protein product		190182	"""transforming growth factor, beta receptor II (70-80kD)"""	MFS2		1319842, 15235604	Standard	NM_001024847		Approved		uc003cen.3	P37173	OTTHUMG00000130569	ENST00000295754.5:c.1167C>T	3.37:g.30713842C>T		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	136	6	0.0441176	NM_001024847	B4DTV5|Q15580|Q6DKT6|Q99474	Silent	SNP	ENST00000295754.5	37	CCDS2648.1																																																																																			C|0.947;T|0.053	0.053	strong		0.557	TGFBR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252994.2		
PPARA	5465	hgsc.bcm.edu	37	22	46615880	46615880	+	Missense_Mutation	SNP	T	T	C	rs1800234	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr22:46615880T>C	ENST00000396000.2	+	6	945	c.680T>C	c.(679-681)gTc>gCc	p.V227A	PPARA_ENST00000262735.5_Missense_Mutation_p.V227A|PPARA_ENST00000407236.1_Missense_Mutation_p.V227A|PPARA_ENST00000434345.2_Intron|PPARA_ENST00000402126.1_Missense_Mutation_p.V227A			Q07869	PPARA_HUMAN	peroxisome proliferator-activated receptor alpha	227			V -> A (in dbSNP:rs1800234).		behavioral response to nicotine (GO:0035095)|cellular lipid metabolic process (GO:0044255)|circadian regulation of gene expression (GO:0032922)|enamel mineralization (GO:0070166)|epidermis development (GO:0008544)|fatty acid metabolic process (GO:0006631)|fatty acid transport (GO:0015908)|gene expression (GO:0010467)|heart development (GO:0007507)|intracellular receptor signaling pathway (GO:0030522)|lipid metabolic process (GO:0006629)|lipoprotein metabolic process (GO:0042157)|negative regulation of appetite (GO:0032099)|negative regulation of blood pressure (GO:0045776)|negative regulation of cholesterol storage (GO:0010887)|negative regulation of glycolytic process (GO:0045820)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|negative regulation of neuron death (GO:1901215)|negative regulation of protein binding (GO:0032091)|negative regulation of receptor biosynthetic process (GO:0010871)|negative regulation of sequestering of triglyceride (GO:0010891)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription regulatory region DNA binding (GO:2000678)|positive regulation of fatty acid beta-oxidation (GO:0032000)|positive regulation of fatty acid oxidation (GO:0046321)|positive regulation of gluconeogenesis (GO:0045722)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cellular ketone metabolic process by positive regulation of transcription from RNA polymerase II promoter (GO:0072366)|regulation of circadian rhythm (GO:0042752)|regulation of glycolytic by positive regulation of transcription from RNA polymerase II promoter (GO:0072363)|regulation of lipid transport by positive regulation of transcription from RNA polymerase II promoter (GO:0072369)|response to hypoxia (GO:0001666)|response to insulin (GO:0032868)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|wound healing (GO:0042060)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|drug binding (GO:0008144)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|lipid binding (GO:0008289)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II repressing transcription factor binding (GO:0001103)|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)|steroid hormone receptor activity (GO:0003707)|ubiquitin conjugating enzyme binding (GO:0031624)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	15		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00522)	Bezafibrate(DB01393)|Clofibrate(DB00636)|Fenofibrate(DB01039)|Gemfibrozil(DB01241)|Indomethacin(DB00328)	AAAGCCCGGGTCATCCTCTCA	0.473													T|||	85	0.0169728	0.0	0.0576	5008	,	,		17524	0.0427		0.001	False		,,,				2504	0.001				p.V227A		Atlas-SNP	.											.	PPARA	36	.	0			c.T680C	GRCh37	CM021318	PPARA	M	rs1800234	PASS	.	T	ALA/VAL,ALA/VAL	1,4405	2.1+/-5.4	0,1,2202	78.0	78.0	78.0		680,680	4.2	0.9	22	dbSNP_89	78	7,8593	5.7+/-21.5	0,7,4293	yes	missense,missense	PPARA	NM_001001928.2,NM_005036.4	64,64	0,8,6495	CC,CT,TT		0.0814,0.0227,0.0615	benign,benign	227/469,227/469	46615880	8,12998	2203	4300	6503	SO:0001583	missense	5465	exon6			CCCGGGTCATCCT	L02932	CCDS33669.1	22q12-q13.1	2013-01-16	2006-10-17		ENSG00000186951	ENSG00000186951		"""Nuclear hormone receptors"""	9232	protein-coding gene	gene with protein product		170998	"""peroxisome proliferative activated receptor, alpha"""	PPAR		7684926, 10591208	Standard	XM_005261655		Approved	hPPAR, NR1C1	uc003bgx.1	Q07869	OTTHUMG00000150443	ENST00000396000.2:c.680T>C	22.37:g.46615880T>C	ENSP00000379322:p.Val227Ala	Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	64	4	0.0625	NM_001001928	B0G0X3|Q16241|Q6I9S0|Q92486|Q92689|Q9Y3N1	Missense_Mutation	SNP	ENST00000396000.2	37	CCDS33669.1	44	0.020146520146520148	0	0.0	12	0.03314917127071823	31	0.05419580419580419	1	0.0013192612137203166	T	0.628	-0.818521	0.02776	2.27E-4	8.14E-4	ENSG00000186951	ENST00000396000;ENST00000262735;ENST00000535613;ENST00000407236;ENST00000402126	T;T;T;T	0.68903	-0.36;-0.36;-0.36;-0.36	5.27	4.22	0.49857	Nuclear hormone receptor, ligand-binding (1);	0.350959	0.33438	N	0.004907	T	0.06050	0.0157	N	0.02539	-0.55	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.11817	-1.0572	10	0.02654	T	1	.	6.3027	0.21121	0.0:0.0799:0.1618:0.7582	rs1800234;rs17847845;rs60636362	227;227	F1D8S4;Q07869	.;PPARA_HUMAN	A	227;227;8;227;227	ENSP00000379322:V227A;ENSP00000262735:V227A;ENSP00000385523:V227A;ENSP00000385246:V227A	ENSP00000262735:V227A	V	+	2	0	PPARA	44994544	0.701000	0.27806	0.929000	0.37066	0.602000	0.36980	0.989000	0.29629	0.807000	0.34208	0.454000	0.30748	GTC	T|0.989;C|0.011	0.011	strong		0.473	PPARA-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318129.3	NM_001001928	
LRCH3	84859	hgsc.bcm.edu	37	3	197597044	197597044	+	Silent	SNP	C	C	T	rs77281724	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr3:197597044C>T	ENST00000425562.2	+	18	1887	c.1887C>T	c.(1885-1887)ccC>ccT	p.P629P	LRCH3_ENST00000536618.1_Silent_p.P224P|LRCH3_ENST00000441090.2_Silent_p.P475P|LRCH3_ENST00000438796.2_Silent_p.P629P|LRCH3_ENST00000334859.4_Silent_p.P629P|LRCH3_ENST00000414675.2_Silent_p.P577P			Q96II8	LRCH3_HUMAN	leucine-rich repeats and calponin homology (CH) domain containing 3	629						cytoplasm (GO:0005737)|extracellular region (GO:0005576)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(13)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29	all_cancers(143;1.15e-09)|Ovarian(172;0.0418)|Breast(254;0.0976)		Epithelial(36;4.82e-24)|all cancers(36;3.61e-22)|OV - Ovarian serous cystadenocarcinoma(49;7.08e-19)|LUSC - Lung squamous cell carcinoma(58;6.94e-07)|Lung(62;9.92e-07)	GBM - Glioblastoma multiforme(93;0.119)		ATGCTTCACCCCTTCCTCCAT	0.443													C|||	506	0.101038	0.1596	0.0648	5008	,	,		20135	0.0069		0.1093	False		,,,				2504	0.136				p.P629P		Atlas-SNP	.											.	LRCH3	96	.	0			c.C1887T						PASS	.	C		548,3858	246.2+/-254.9	27,494,1682	129.0	137.0	134.0		1887	1.2	0.8	3	dbSNP_132	134	978,7622	211.4+/-252.0	52,874,3374	no	coding-synonymous	LRCH3	NM_032773.2		79,1368,5056	TT,TC,CC		11.3721,12.4376,11.733		629/713	197597044	1526,11480	2203	4300	6503	SO:0001819	synonymous_variant	84859	exon18			TTCACCCCTTCCT	AL137527	CCDS3330.1	3q29	2006-04-12			ENSG00000186001	ENSG00000186001			28637	protein-coding gene	gene with protein product						12477932	Standard	NM_032773		Approved	MGC4126	uc003fyj.1	Q96II8	OTTHUMG00000155378	ENST00000425562.2:c.1887C>T	3.37:g.197597044C>T		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	79	4	0.0506329	NM_032773	B4E0T7|Q96FP9|Q9NT52	Silent	SNP	ENST00000425562.2	37		191	0.08745421245421245	78	0.15853658536585366	22	0.06077348066298342	6	0.01048951048951049	85	0.11213720316622691	C	3.141	-0.176262	0.06380	0.124376	0.113721	ENSG00000186001	ENST00000428136	T	0.47528	0.84	5.19	1.25	0.21368	.	0.615691	0.15074	N	0.282036	T	0.00109	0.0003	.	.	.	0.09310	P	0.99999999467511	.	.	.	.	.	.	T	0.10613	-1.0622	6	0.22706	T	0.39	-0.7417	1.8562	0.03179	0.4717:0.2482:0.1542:0.1259	.	.	.	.	S	7	ENSP00000394763:P7S	ENSP00000394763:P7S	P	+	1	0	LRCH3	199081441	0.438000	0.25602	0.807000	0.32361	0.331000	0.28603	-0.359000	0.07632	0.167000	0.19631	-0.187000	0.12897	CCT	C|0.887;T|0.113	0.113	strong		0.443	LRCH3-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000339965.1	NM_032773	
ZNF844	284391	hgsc.bcm.edu	37	19	12186857	12186857	+	Missense_Mutation	SNP	G	G	C	rs6511763	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr19:12186857G>C	ENST00000439326.3	+	4	1097	c.922G>C	c.(922-924)Gct>Cct	p.A308P	ZNF844_ENST00000441304.2_3'UTR	NM_001136501.1	NP_001129973.1	Q08AG5	ZN844_HUMAN	zinc finger protein 844	308			A -> P (in dbSNP:rs6511763).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|lung(1)|prostate(1)	10						TGAGGAGAAGGCTTATGAATG	0.413													.|||	1455	0.290535	0.73	0.1455	5008	,	,		21988	0.0853		0.161	False		,,,				2504	0.1442				p.A308P		Atlas-SNP	.											.	ZNF844	69	.	0			c.G922C						PASS	.	C	PRO/ALA	887,497		287,313,92	67.0	64.0	65.0		922	1.4	0.0	19	dbSNP_116	65	416,2766		25,366,1200	yes	missense	ZNF844	NM_001136501.1	27	312,679,1292	CC,CG,GG		13.0735,35.9104,28.537	benign	308/667	12186857	1303,3263	692	1591	2283	SO:0001583	missense	284391	exon4			GAGAAGGCTTATG	AL832297	CCDS45985.1	19p13.2	2013-01-08			ENSG00000223547	ENSG00000223547		"""Zinc fingers, C2H2-type"", ""-"""	25932	protein-coding gene	gene with protein product							Standard	NM_001136501		Approved	FLJ14959	uc002mtb.2	Q08AG5	OTTHUMG00000156405	ENST00000439326.3:c.922G>C	19.37:g.12186857G>C	ENSP00000392024:p.Ala308Pro	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	147	6	0.0408163	NM_001136501	Q5JPI8	Missense_Mutation	SNP	ENST00000439326.3	37	CCDS45985.1	572	0.2619047619047619	339	0.6890243902439024	53	0.1464088397790055	53	0.09265734265734266	127	0.16754617414248021	C	1.412	-0.575281	0.03882	0.640896	0.130735	ENSG00000223547	ENST00000439326;ENST00000541708;ENST00000535505	T	0.10192	2.9	2.5	1.42	0.22433	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.00047	-2.43	0.26978	P	0.9654259	B	0.02656	0.0	B	0.01281	0.0	T	0.33929	-0.9849	8	0.02654	T	1	.	5.9876	0.19442	0.0:0.6833:0.1951:0.1217	rs6511763;rs52826403;rs60463492;rs6511763	308	Q08AG5	ZN844_HUMAN	P	308;308;283	ENSP00000392024:A308P	ENSP00000392024:A308P	A	+	1	0	ZNF844	12047857	0.000000	0.05858	0.001000	0.08648	0.403000	0.30841	0.066000	0.14489	-0.014000	0.14175	-0.980000	0.02579	GCT	G|0.739;C|0.261	0.261	strong		0.413	ZNF844-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344086.2		
RGS22	26166	hgsc.bcm.edu	37	8	101011612	101011612	+	Missense_Mutation	SNP	G	G	A	rs3133711	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr8:101011612G>A	ENST00000360863.6	-	19	3021	c.2827C>T	c.(2827-2829)Cat>Tat	p.H943Y	RGS22_ENST00000523437.1_Missense_Mutation_p.H931Y|RGS22_ENST00000519421.1_5'Flank|RGS22_ENST00000523287.1_Missense_Mutation_p.H762Y	NM_015668.3	NP_056483.3	Q8NE09	RGS22_HUMAN	regulator of G-protein signaling 22	943	RGS 1. {ECO:0000255|PROSITE- ProRule:PRU00171}.		H -> Y (in dbSNP:rs3133711).		positive regulation of GTPase activity (GO:0043547)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)		RGS22/SYCP1(2)	breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(33)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	68			Epithelial(11;6.71e-08)|all cancers(13;4.19e-06)|OV - Ovarian serous cystadenocarcinoma(57;0.000469)|STAD - Stomach adenocarcinoma(118;0.169)			AGCTGCTCATGAAGAATCTTC	0.373													G|||	183	0.0365415	0.0129	0.0432	5008	,	,		18591	0.1042		0.0	False		,,,				2504	0.0317				p.H943Y		Atlas-SNP	.											.	RGS22	319	.	0			c.C2827T						PASS	.	G	TYR/HIS	33,3679		0,33,1823	98.0	90.0	92.0		2827	4.7	1.0	8	dbSNP_103	92	3,8235		0,3,4116	yes	missense	RGS22	NM_015668.3	83	0,36,5939	AA,AG,GG		0.0364,0.889,0.3013	possibly-damaging	943/1265	101011612	36,11914	1856	4119	5975	SO:0001583	missense	26166	exon19			GCTCATGAAGAAT	AY009106	CCDS43758.1, CCDS69521.1, CCDS75775.1	8q22.2	2014-01-21	2007-08-14		ENSG00000132554	ENSG00000132554		"""Regulators of G-protein signaling"""	24499	protein-coding gene	gene with protein product		615650	"""regulator of G-protein signalling 22"""				Standard	XM_005250856		Approved	DKFZP434I092, PRTD-NY2, CT145	uc003yjb.1	Q8NE09	OTTHUMG00000164802	ENST00000360863.6:c.2827C>T	8.37:g.101011612G>A	ENSP00000354109:p.His943Tyr	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	92	4	0.0434783	NM_015668	A8K944|Q569L2|Q86Y71|Q9BYZ4|Q9UFN6	Missense_Mutation	SNP	ENST00000360863.6	37	CCDS43758.1	85	0.03891941391941392	6	0.012195121951219513	10	0.027624309392265192	69	0.12062937062937062	0	0.0	G	21.4	4.139548	0.77775	0.00889	3.64E-4	ENSG00000132554	ENST00000360863;ENST00000427793;ENST00000523287;ENST00000523437;ENST00000517828	T;T;T;T	0.47869	1.92;1.92;1.92;0.83	4.72	4.72	0.59763	Regulator of G protein signalling (3);Regulator of G protein signalling superfamily (1);	0.079005	0.52532	D	0.000062	T	0.02119	0.0066	M	0.68317	2.08	0.36094	D	0.843658	D;D;D	0.76494	0.999;0.999;0.997	D;D;D	0.79784	0.993;0.993;0.957	T	0.48525	-0.9028	10	0.66056	D	0.02	.	17.6791	0.88238	0.0:0.0:1.0:0.0	rs3133711;rs3133711	931;943;762	A8K944;Q8NE09;G3V112	.;RGS22_HUMAN;.	Y	943;930;762;931;258	ENSP00000354109:H943Y;ENSP00000429382:H762Y;ENSP00000428212:H931Y;ENSP00000427754:H258Y	ENSP00000354109:H943Y	H	-	1	0	RGS22	101080788	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	7.126000	0.77201	2.147000	0.66899	0.655000	0.94253	CAT	G|0.964;A|0.036	0.036	strong		0.373	RGS22-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000380365.1	NM_015668	
FAM162B	221303	hgsc.bcm.edu	37	6	117086652	117086652	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr6:117086652G>A	ENST00000368557.4	-	1	234	c.88C>T	c.(88-90)Cgg>Tgg	p.R30W		NM_001085480.2	NP_001078949.1	Q5T6X4	F162B_HUMAN	family with sequence similarity 162, member B	30						integral component of membrane (GO:0016021)				large_intestine(2)|lung(4)	6						GGTGCGGGCCGTCGCGTGGCC	0.746																																					p.R30W		Atlas-SNP	.											.	FAM162B	19	.	0			c.C88T						PASS	.						2.0	3.0	3.0					6																	117086652		1446	3410	4856	SO:0001583	missense	221303	exon1			CGGGCCGTCGCGT	BC038997	CCDS43497.1	6q22.31	2014-01-28	2008-06-05	2008-06-05	ENSG00000183807	ENSG00000183807			21549	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 189"""	C6orf189			Standard	NM_001085480		Approved	bA86F4.2	uc003pxi.2	Q5T6X4	OTTHUMG00000015446	ENST00000368557.4:c.88C>T	6.37:g.117086652G>A	ENSP00000357545:p.Arg30Trp	Somatic	23	0	0		WXS	Illumina HiSeq	Phase_I	13	7	0.538462	NM_001085480	Q8IXW8	Missense_Mutation	SNP	ENST00000368557.4	37	CCDS43497.1	.	.	.	.	.	.	.	.	.	.	G	9.606	1.129940	0.21041	.	.	ENSG00000183807	ENST00000368557	T	0.31769	1.48	2.93	-3.02	0.05446	.	0.936775	0.08728	N	0.902552	T	0.05135	0.0137	N	0.17474	0.49	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.39354	-0.9618	10	0.46703	T	0.11	0.0041	4.5061	0.11889	0.4972:0.2298:0.273:0.0	.	30	Q5T6X4	F162B_HUMAN	W	30	ENSP00000357545:R30W	ENSP00000357545:R30W	R	-	1	2	FAM162B	117193345	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.029000	0.12329	-0.773000	0.04596	-0.643000	0.03959	CGG	.	.	none		0.746	FAM162B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041965.1	XM_927381	
SOCS6	9306	hgsc.bcm.edu	37	18	67992810	67992810	+	Silent	SNP	G	G	T			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr18:67992810G>T	ENST00000397942.3	+	2	1222	c.906G>T	c.(904-906)gcG>gcT	p.A302A	SOCS6_ENST00000582322.1_Silent_p.A302A	NM_004232.3	NP_004223.2	O14544	SOCS6_HUMAN	suppressor of cytokine signaling 6	302					defense response (GO:0006952)|JAK-STAT cascade (GO:0007259)|negative regulation of signal transduction (GO:0009968)|negative regulation of T cell activation (GO:0050868)|proteasomal protein catabolic process (GO:0010498)|protein ubiquitination (GO:0016567)|regulation of growth (GO:0040008)	cytoplasm (GO:0005737)|immunological synapse (GO:0001772)				NS(1)|breast(2)|endometrium(1)|kidney(2)|large_intestine(4)|lung(9)|ovary(1)|prostate(2)	22		Esophageal squamous(42;0.129)|Colorectal(73;0.152)				GCCCGAGAGCGGGTCACGATG	0.532																																					p.A302A	Melanoma(84;1024 1361 24382 36583 42651)	Atlas-SNP	.											SOCS6,NS,carcinoma,+2,1	SOCS6	54	1	0			c.G906T						scavenged	.						126.0	115.0	119.0					18																	67992810		2203	4300	6503	SO:0001819	synonymous_variant	9306	exon2			GAGAGCGGGTCAC	AB006968	CCDS11998.1	18q22	2013-02-14	2004-02-25	2004-02-27	ENSG00000170677	ENSG00000170677		"""Suppressors of cytokine signaling"", ""SH2 domain containing"""	16833	protein-coding gene	gene with protein product		605118	"""suppressor of cytokine signaling 4"""	SOCS4		9344848, 11042152	Standard	NM_004232		Approved	CIS4, SSI4, HSPC060, STATI4, STAI4, Cish4	uc002lkr.1	O14544	OTTHUMG00000132816	ENST00000397942.3:c.906G>T	18.37:g.67992810G>T		Somatic	115	1	0.00869565		WXS	Illumina HiSeq	Phase_I	113	3	0.0265487	NM_004232	Q8WUM3	Silent	SNP	ENST00000397942.3	37	CCDS11998.1																																																																																			.	.	none		0.532	SOCS6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256270.2		
XAF1	54739	hgsc.bcm.edu	37	17	6663894	6663894	+	Missense_Mutation	SNP	G	G	A	rs386794960|rs2271232	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr17:6663894G>A	ENST00000361842.3	+	4	634	c.395G>A	c.(394-396)cGc>cAc	p.R132H	XAF1_ENST00000346752.4_Missense_Mutation_p.R113H|XAF1_ENST00000438512.1_Missense_Mutation_p.R132H|XAF1_ENST00000441631.1_Missense_Mutation_p.R132H	NM_017523.3	NP_059993.2	Q6GPH4	XAF1_HUMAN	XIAP associated factor 1	132			R -> H (in dbSNP:rs2271232).	R -> Q (in Ref. 3; BAF85537). {ECO:0000305}.	apoptotic process (GO:0006915)|cytokine-mediated signaling pathway (GO:0019221)|negative regulation of protein complex assembly (GO:0031333)|response to interferon-beta (GO:0035456)|type I interferon signaling pathway (GO:0060337)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			large_intestine(2)|lung(2)|prostate(1)|urinary_tract(1)	6						GATGTCTGTCGCAGTGAACAG	0.592													G|||	670	0.133786	0.2481	0.072	5008	,	,		17101	0.1855		0.0398	False		,,,				2504	0.0665				p.R132H		Atlas-SNP	.											XAF1,colon,carcinoma,+1,1	XAF1	16	1	0			c.G395A						scavenged	.						51.0	50.0	50.0					17																	6663894		2203	4300	6503	SO:0001583	missense	54739	exon4			TCTGTCGCAGTGA	X99699	CCDS11080.1, CCDS11081.1	17p13.2	2010-03-19			ENSG00000132530	ENSG00000132530			30932	protein-coding gene	gene with protein product		606717				12029096, 11175744	Standard	NM_199139		Approved	BIRC4BP, XIAPAF1, HSXIAPAF1	uc002gdn.3	Q6GPH4		ENST00000361842.3:c.395G>A	17.37:g.6663894G>A	ENSP00000354822:p.Arg132His	Somatic	218	2	0.00917431		WXS	Illumina HiSeq	Phase_I	202	7	0.0346535	NM_017523	A2T931|A2T932|A8K2L1|A8K9Y3|D3DTM6|Q6MZE8|Q8N557|Q99982	Missense_Mutation	SNP	ENST00000361842.3	37	CCDS11080.1	220	0.10073260073260074	98	0.1991869918699187	17	0.04696132596685083	76	0.13286713286713286	29	0.03825857519788918	G	14.62	2.589297	0.46214	.	.	ENSG00000132530	ENST00000361842;ENST00000441631;ENST00000346752;ENST00000438512	T;T;T;T	0.29397	1.57;1.57;1.57;1.57	3.77	-4.73	0.03259	.	1.042900	0.07588	N	0.921505	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	D;D;P;D	0.62365	0.991;0.974;0.956;0.963	P;B;B;B	0.47430	0.547;0.4;0.2;0.301	T	0.05099	-1.0906	9	0.38643	T	0.18	-0.2545	5.9149	0.19050	0.297:0.0:0.5538:0.1493	rs2271232	132;113;132;72	C9J7Z8;Q6GPH4-2;Q6GPH4;B3KPW1	.;.;XAF1_HUMAN;.	H	132;132;113;132	ENSP00000354822:R132H;ENSP00000413199:R132H;ENSP00000341029:R113H;ENSP00000406233:R132H	ENSP00000341029:R113H	R	+	2	0	XAF1	6604618	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-1.822000	0.01711	-0.958000	0.03622	0.455000	0.32223	CGC	G|0.925;A|0.075	0.075	strong		0.592	XAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439643.5	NM_017523	
RNF145	153830	hgsc.bcm.edu	37	5	158630642	158630642	+	5'UTR	SNP	T	T	C	rs74770414|rs202186112		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr5:158630642T>C	ENST00000424310.2	-	0	343				RNF145_ENST00000519865.1_5'UTR|RNF145_ENST00000518802.1_Missense_Mutation_p.K25R|RNF145_ENST00000520638.1_Missense_Mutation_p.K9R|RNF145_ENST00000274542.2_Missense_Mutation_p.K23R|RNF145_ENST00000521606.2_Missense_Mutation_p.K12R	NM_001199383.1	NP_001186312.1	Q96MT1	RN145_HUMAN	ring finger protein 145							integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)			endometrium(7)|kidney(2)|large_intestine(5)|lung(9)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	30	Renal(175;0.00196)	Medulloblastoma(196;0.0523)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			tttttttttcttttttttttt	0.363																																					p.K25R		Atlas-SNP	.											RNF145,NS,carcinoma,0,2	RNF145	110	2	0			c.A74G						scavenged	.						31.0	34.0	33.0					5																	158630642		2202	4300	6502	SO:0001623	5_prime_UTR_variant	153830	exon2			TTTTTCTTTTTTT	BC042684	CCDS4344.1, CCDS56390.1, CCDS56391.1, CCDS56392.1, CCDS56393.1	5q33.3	2013-01-09			ENSG00000145860	ENSG00000145860		"""RING-type (C3HC4) zinc fingers"""	20853	protein-coding gene	gene with protein product							Standard	NM_001199380		Approved	FLJ31951	uc003lxo.2	Q96MT1	OTTHUMG00000130306	ENST00000424310.2:c.-17A>G	5.37:g.158630642T>C		Somatic	77	1	0.012987		WXS	Illumina HiSeq	Phase_I	74	4	0.0540541	NM_001199380	B7Z903|B7Z949|E7EVI7|Q8IVP7	Missense_Mutation	SNP	ENST00000424310.2	37	CCDS56390.1	.	.	.	.	.	.	.	.	.	.	T	0.109	-1.141491	0.01728	.	.	ENSG00000145860	ENST00000274542;ENST00000521606;ENST00000413445;ENST00000518802;ENST00000520638	T;T;T;T;T	0.77229	-1.07;-1.06;-1.05;-1.08;-1.05	2.19	-4.37	0.03633	.	6.604780	0.00166	N	0.000010	T	0.49508	0.1561	N	0.08118	0	0.09310	N	0.999998	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.01281	0.0;0.0;0.0;0.0;0.0	T	0.56282	-0.8005	10	0.02654	T	1	.	0.9232	0.01319	0.1799:0.1427:0.3534:0.324	.	11;12;9;25;23	E7EW26;B7Z949;B7Z903;E7EVI7;Q96MT1-2	.;.;.;.;.	R	23;11;12;25;9	ENSP00000274542:K23R;ENSP00000430753:K11R;ENSP00000445115:K12R;ENSP00000430955:K25R;ENSP00000429071:K9R	ENSP00000274542:K23R	K	-	2	0	RNF145	158563220	0.009000	0.17119	0.000000	0.03702	0.001000	0.01503	1.862000	0.39448	-2.940000	0.00297	-1.381000	0.01174	AAG	.	.	weak		0.363	RNF145-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374048.1	NM_144726	
TAS2R20	259295	hgsc.bcm.edu	37	12	11149711	11149711	+	Missense_Mutation	SNP	C	C	A	rs10845279	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr12:11149711C>A	ENST00000538986.1	-	1	763	c.764G>T	c.(763-765)cGa>cTa	p.R255L	PRR4_ENST00000536668.1_Intron|TAS2R14_ENST00000381852.4_Intron	NM_176889.2	NP_795370.2	P59543	T2R20_HUMAN	taste receptor, type 2, member 20	255			R -> L (in dbSNP:rs10845279). {ECO:0000269|PubMed:15496549}.		sensory perception of taste (GO:0050909)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.R255Q(1)		breast(1)|endometrium(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	13						TTCTTTTGGTCGCATCTTAAA	0.373													C|||	2119	0.423123	0.0651	0.3847	5008	,	,		18928	0.755		0.3827	False		,,,				2504	0.6339				p.R255L		Atlas-SNP	.											TAS2R20,colon,carcinoma,0,1	TAS2R20	17	1	1	Substitution - Missense(1)	large_intestine(1)	c.G764T						scavenged	.	C	LEU/ARG	442,3964	212.8+/-232.6	18,406,1779	110.0	109.0	109.0		764	-5.3	0.0	12	dbSNP_120	109	3016,5584	465.2+/-366.4	544,1928,1828	yes	missense	TAS2R20	NM_176889.2	102	562,2334,3607	AA,AC,CC		35.0698,10.0318,26.5877	benign	255/310	11149711	3458,9548	2203	4300	6503	SO:0001583	missense	259295	exon1			TTTGGTCGCATCT	AX097732, AF494236	CCDS8639.1	12p13.2	2012-08-22			ENSG00000255837	ENSG00000255837		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	19109	protein-coding gene	gene with protein product		613962	"""taste receptor, type 2, member 49"""	TAS2R49			Standard	NM_176889		Approved	T2R20, T2R56	uc001qzm.2	P59543	OTTHUMG00000162695	ENST00000538986.1:c.764G>T	12.37:g.11149711C>A	ENSP00000441624:p.Arg255Leu	Somatic	241	0	0		WXS	Illumina HiSeq	Phase_I	225	8	0.0355556	NM_176889	P59549|Q2HIZ4|Q496D8|Q645X9	Missense_Mutation	SNP	ENST00000538986.1	37	CCDS8639.1	898	0.41117216117216115	33	0.06707317073170732	155	0.4281767955801105	426	0.7447552447552448	284	0.37467018469656993	C	0.008	-1.921931	0.00498	0.100318	0.350698	ENSG00000255837	ENST00000538986	T	0.00753	5.74	2.66	-5.32	0.02722	.	2.067560	0.05057	N	0.479233	T	0.00012	0.0000	N	0.00017	-2.83	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.46638	-0.9177	9	0.02654	T	1	.	4.8332	0.13451	0.2999:0.1236:0.0:0.5765	rs10845279;rs60755728;rs10845279	255	P59543	T2R20_HUMAN	L	255	ENSP00000441624:R255L	ENSP00000441624:R255L	R	-	2	0	TAS2R20	11040978	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.312000	0.02720	-1.408000	0.02040	-0.383000	0.06682	CGA	C|0.671;A|0.329	0.329	strong		0.373	TAS2R20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370130.2	NM_176889	
PCDHGA1	56114	hgsc.bcm.edu	37	5	140711241	140711241	+	Missense_Mutation	SNP	A	A	C			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr5:140711241A>C	ENST00000517417.1	+	1	990	c.990A>C	c.(988-990)aaA>aaC	p.K330N	AC005618.6_ENST00000606901.1_lincRNA|PCDHGA1_ENST00000378105.3_Missense_Mutation_p.K330N	NM_018912.2	NP_061735.1	Q9Y5H4	PCDG1_HUMAN	protocadherin gamma subfamily A, 1	330	Cadherin 3. {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(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(18)|lung(32)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TCATGGCTAAAGTTAAGGTAC	0.418																																					p.K330N		Atlas-SNP	.											.	PCDHGA1	397	.	0			c.A990C						PASS	.						70.0	69.0	70.0					5																	140711241		2203	4300	6503	SO:0001583	missense	56114	exon1			GGCTAAAGTTAAG	AF152318	CCDS54922.1	5q31	2010-01-26				ENSG00000204956		"""Cadherins / Protocadherins : Clustered"""	8696	other	protocadherin		606288				10380929	Standard	NM_018912		Approved	PCDH-GAMMA-A1		Q9Y5H4		ENST00000517417.1:c.990A>C	5.37:g.140711241A>C	ENSP00000431083:p.Lys330Asn	Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	183	26	0.142077	NM_018912	Q2M273|Q9Y5D6	Missense_Mutation	SNP	ENST00000517417.1	37	CCDS54922.1	.	.	.	.	.	.	.	.	.	.	A	1.463	-0.561832	0.03939	.	.	ENSG00000204956	ENST00000517417;ENST00000378105	T;T	0.01838	4.61;4.61	3.99	2.81	0.32909	Cadherin (5);Cadherin-like (1);	0.118831	0.37348	N	0.002129	T	0.01222	0.0040	N	0.08118	0	0.09310	N	1	B;P	0.34815	0.061;0.47	B;B	0.33121	0.038;0.158	T	0.47873	-0.9083	10	0.72032	D	0.01	.	2.7623	0.05310	0.5109:0.0:0.1932:0.2958	.	330;330	Q9Y5H4-2;Q9Y5H4	.;PCDG1_HUMAN	N	330	ENSP00000431083:K330N;ENSP00000367345:K330N	ENSP00000367345:K330N	K	+	3	2	PCDHGA1	140691425	0.000000	0.05858	0.999000	0.59377	0.094000	0.18550	-1.649000	0.01993	0.698000	0.31739	-0.297000	0.09499	AAA	.	.	none		0.418	PCDHGA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000374737.1	NM_018912	
TAPT1	202018	hgsc.bcm.edu	37	4	16188159	16188159	+	Splice_Site	SNP	G	G	T			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr4:16188159G>T	ENST00000405303.2	-	7	998	c.915C>A	c.(913-915)agC>agA	p.S305R	TAPT1_ENST00000399920.3_Splice_Site_p.S194R|TAPT1_ENST00000304584.8_Splice_Site_p.S86R|TAPT1_ENST00000508888.1_5'Flank	NM_153365.2	NP_699196.2	Q6NXT6	TAPT1_HUMAN	transmembrane anterior posterior transformation 1	305					embryonic skeletal system development (GO:0048706)|G-protein coupled receptor signaling pathway (GO:0007186)|in utero embryonic development (GO:0001701)|post-embryonic development (GO:0009791)	integral component of membrane (GO:0016021)	growth hormone-releasing hormone receptor activity (GO:0016520)			NS(1)|breast(2)|cervix(1)|kidney(2)|large_intestine(2)|lung(1)|prostate(1)	10						TGTACATACCGCTATTTGACA	0.328																																					p.S305R		Atlas-SNP	.											TAPT1,NS,carcinoma,0,2	TAPT1	31	2	0			c.C915A						scavenged	.						90.0	84.0	86.0					4																	16188159		1787	3967	5754	SO:0001630	splice_region_variant	202018	exon7			CATACCGCTATTT	AK074494	CCDS47030.1	4p15.32	2014-01-28			ENSG00000169762	ENSG00000169762			26887	protein-coding gene	gene with protein product		612758				12477932	Standard	NM_153365		Approved	FLJ90013	uc010ied.1	Q6NXT6	OTTHUMG00000160177	ENST00000405303.2:c.916+1C>A	4.37:g.16188159G>T		Somatic	399	2	0.00501253		WXS	Illumina HiSeq	Phase_I	404	5	0.0123762	NM_153365	Q8N2S3|Q9NZK9	Missense_Mutation	SNP	ENST00000405303.2	37	CCDS47030.1	.	.	.	.	.	.	.	.	.	.	G	13.14	2.148486	0.37923	.	.	ENSG00000169762	ENST00000405303;ENST00000542770;ENST00000399920;ENST00000304584	T;T	0.35973	1.28;1.32	5.46	-5.08	0.02929	.	0.000000	0.85682	D	0.000000	T	0.50531	0.1621	M	0.81341	2.54	0.80722	D	1	D	0.56287	0.975	P	0.57009	0.811	T	0.60637	-0.7224	10	0.59425	D	0.04	-0.0368	15.2372	0.73441	0.6607:0.0:0.3393:0.0	.	305	Q6NXT6	TAPT1_HUMAN	R	305;305;194;86	ENSP00000385347:S305R;ENSP00000382803:S194R	ENSP00000305198:S86R	S	-	3	2	TAPT1	15797257	0.397000	0.25270	0.874000	0.34290	0.261000	0.26267	-0.109000	0.10840	-1.280000	0.02402	-1.974000	0.00461	AGC	.	.	none		0.328	TAPT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359568.1	NM_153365	Missense_Mutation
CATSPERD	257062	hgsc.bcm.edu	37	19	5778597	5778597	+	Silent	SNP	C	C	G	rs2305926	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr19:5778597C>G	ENST00000381624.3	+	22	2368	c.2307C>G	c.(2305-2307)gtC>gtG	p.V769V	CATSPERD_ENST00000309164.7_3'UTR	NM_152784.3	NP_689997.3	Q86XM0	CTSRD_HUMAN	catsper channel auxiliary subunit delta	769					multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|single fertilization (GO:0007338)|sperm capacitation (GO:0048240)|sperm motility (GO:0030317)|sperm-egg recognition (GO:0035036)|spermatogenesis (GO:0007283)	CatSper complex (GO:0036128)|plasma membrane (GO:0005886)|sperm principal piece (GO:0097228)		p.V769V(1)									GCAAGACGGTCTGCCAGTTCA	0.652													C|||	156	0.0311502	0.0	0.013	5008	,	,		15814	0.0843		0.0179	False		,,,				2504	0.045				p.V769V		Atlas-SNP	.											TMEM146,NS,carcinoma,0,1	.	.	1	1	Substitution - coding silent(1)	lung(1)	c.C2307G						PASS	.	C		20,4264		0,20,2122	55.0	63.0	60.0		2307	-5.7	0.0	19	dbSNP_100	60	123,8337		1,121,4108	no	coding-synonymous	TMEM146	NM_152784.3		1,141,6230	GG,GC,CC		1.4539,0.4669,1.1221		769/799	5778597	143,12601	2142	4230	6372	SO:0001819	synonymous_variant	257062	exon22			GACGGTCTGCCAG	BC043005	CCDS12149.2	19p13.3	2013-10-11	2012-02-22	2012-02-22	ENSG00000174898	ENSG00000174898			28598	protein-coding gene	gene with protein product			"""transmembrane protein 146"""	TMEM146		21224844	Standard	NM_152784		Approved	MGC39581	uc002mda.3	Q86XM0	OTTHUMG00000143036	ENST00000381624.3:c.2307C>G	19.37:g.5778597C>G		Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	148	9	0.0608108	NM_152784	Q6ZRP1	Silent	SNP	ENST00000381624.3	37	CCDS12149.2																																																																																			C|0.978;G|0.022	0.022	strong		0.652	CATSPERD-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000286953.2	NM_152784	
NLRP5	126206	hgsc.bcm.edu	37	19	56552307	56552307	+	Missense_Mutation	SNP	A	A	C			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr19:56552307A>C	ENST00000390649.3	+	11	2806	c.2806A>C	c.(2806-2808)Aca>Cca	p.T936P		NM_153447.4	NP_703148.4	P59047	NALP5_HUMAN	NLR family, pyrin domain containing 5	936					cellular protein complex assembly (GO:0043623)|cellular protein localization (GO:0034613)|embryo implantation (GO:0007566)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|neuron death (GO:0070997)|organ morphogenesis (GO:0009887)|regulation of protein stability (GO:0031647)|regulation of RNA stability (GO:0043487)	apical cortex (GO:0045179)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|protein complex (GO:0043234)	ATP binding (GO:0005524)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|ovary(5)|skin(2)|stomach(4)|upper_aerodigestive_tract(2)	25		Colorectal(82;3.46e-05)|Ovarian(87;0.0481)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0326)		CTGTGGCATCACAGCCACGGG	0.542																																					p.T936P		Atlas-SNP	.											.	NLRP5	217	.	0			c.A2806C						PASS	.						69.0	69.0	69.0					19																	56552307		2005	4191	6196	SO:0001583	missense	126206	exon11			GGCATCACAGCCA	AY154460	CCDS12938.1	19q13.43	2008-10-30	2006-12-08	2006-12-08	ENSG00000171487	ENSG00000171487		"""Nucleotide-binding domain and leucine rich repeat containing"""	21269	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 5"""	609658	"""NACHT, leucine rich repeat and PYD containing 5"""	NALP5		12563287, 11925379	Standard	NM_153447		Approved	PYPAF8, MATER, PAN11, CLR19.8	uc002qmj.3	P59047	OTTHUMG00000149887	ENST00000390649.3:c.2806A>C	19.37:g.56552307A>C	ENSP00000375063:p.Thr936Pro	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	58	6	0.103448	NM_153447	A8MTY4|Q86W29	Missense_Mutation	SNP	ENST00000390649.3	37	CCDS12938.1	.	.	.	.	.	.	.	.	.	.	A	13.03	2.114132	0.37339	.	.	ENSG00000171487	ENST00000390649	T	0.57107	0.42	4.37	-2.11	0.07187	.	0.889887	0.09138	N	0.843342	T	0.59783	0.2219	M	0.90595	3.13	0.09310	N	0.999999	B	0.32543	0.375	B	0.42653	0.394	T	0.60712	-0.7209	10	0.66056	D	0.02	.	1.426	0.02323	0.3361:0.1463:0.0903:0.4272	.	936	P59047	NALP5_HUMAN	P	936	ENSP00000375063:T936P	ENSP00000375063:T936P	T	+	1	0	NLRP5	61244119	0.000000	0.05858	0.001000	0.08648	0.000000	0.00434	-1.019000	0.03622	-0.685000	0.05177	-1.155000	0.01812	ACA	.	.	none		0.542	NLRP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313735.1	NM_153447	
IQSEC2	23096	hgsc.bcm.edu	37	X	53280102	53280102	+	Silent	SNP	C	C	T	rs200411197		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chrX:53280102C>T	ENST00000375368.5	-	4	1826	c.1626G>A	c.(1624-1626)ccG>ccA	p.P542P	IQSEC2_ENST00000396435.3_Silent_p.P552P|IQSEC2_ENST00000375365.2_Silent_p.P347P			Q5JU85	IQEC2_HUMAN	IQ motif and Sec7 domain 2	542	Pro-rich.				actin cytoskeleton organization (GO:0030036)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(10)|ovary(4)|skin(1)	29						GAGGAACTGGCGGGAGAGGGG	0.672													c|||	1	0.000264901	0.0	0.0	3775	,	,		10478	0.001		0.0	False		,,,				2504	0.0				p.P552P		Atlas-SNP	.											.	IQSEC2	195	.	0			c.G1656A						PASS	.						20.0	24.0	23.0					X																	53280102		2200	4283	6483	SO:0001819	synonymous_variant	23096	exon5			AACTGGCGGGAGA	AB011094	CCDS35298.1, CCDS48130.1	Xp11.23	2014-01-31			ENSG00000124313	ENSG00000124313			29059	protein-coding gene	gene with protein product		300522	"""mental retardation, X-linked 1 (non-dysmorphic)"""	MRX1		9628581, 20473311	Standard	NM_001243197		Approved	KIAA0522	uc004dsd.3	Q5JU85	OTTHUMG00000021608	ENST00000375368.5:c.1626G>A	X.37:g.53280102C>T		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	120	7	0.0583333	NM_001111125	B3KT97|C7SDG1|O60275|Q5JUX1	Silent	SNP	ENST00000375368.5	37																																																																																				C|1.000;T|0.000	0.000	strong		0.672	IQSEC2-201	KNOWN	basic	protein_coding	protein_coding		XM_291345	
FREM1	158326	hgsc.bcm.edu	37	9	14747412	14747412	+	Silent	SNP	A	A	G	rs4741426	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr9:14747412A>G	ENST00000380880.3	-	33	6642	c.5859T>C	c.(5857-5859)gtT>gtC	p.V1953V	FREM1_ENST00000380894.1_Silent_p.V489V|FREM1_ENST00000422223.2_Silent_p.V1953V|FREM1_ENST00000380881.4_Silent_p.V1954V			Q5H8C1	FREM1_HUMAN	FRAS1 related extracellular matrix 1	1953					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)		GTTTCAAGGAAACTATCCCAT	0.368													A|||	688	0.13738	0.0076	0.2161	5008	,	,		17179	0.1806		0.1839	False		,,,				2504	0.1646				p.V1953V		Atlas-SNP	.											.	FREM1	261	.	0			c.T5859C						PASS	.	A	,	158,3628		3,152,1738	114.0	99.0	103.0		1467,5859	-0.1	0.1	9	dbSNP_111	103	1590,6650		151,1288,2681	no	coding-synonymous,coding-synonymous	FREM1	NM_001177704.1,NM_144966.5	,	154,1440,4419	GG,GA,AA		19.2961,4.1733,14.5352	,	489/716,1953/2180	14747412	1748,10278	1893	4120	6013	SO:0001819	synonymous_variant	158326	exon34			CAAGGAAACTATC	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.5859T>C	9.37:g.14747412A>G		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	133	7	0.0526316	NM_144966	B7ZBX4|Q5VV00|Q5VV01|Q6MZI4|Q8NEG9|Q96LI3	Silent	SNP	ENST00000380880.3	37	CCDS47952.1																																																																																			A|0.848;G|0.152	0.152	strong		0.368	FREM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339474.2	NM_144966	
PEG3	5178	hgsc.bcm.edu	37	19	57325083	57325083	+	Missense_Mutation	SNP	C	C	T	rs34051133	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr19:57325083C>T	ENST00000326441.9	-	10	5090	c.4727G>A	c.(4726-4728)cGc>cAc	p.R1576H	PEG3_ENST00000593695.1_Missense_Mutation_p.R1450H|PEG3_ENST00000423103.2_Missense_Mutation_p.R1576H|ZIM2_ENST00000599935.1_Intron|ZIM2_ENST00000391708.3_Intron|ZIM2_ENST00000221722.5_Intron|ZIM2_ENST00000601070.1_Intron|ZIM2_ENST00000593711.1_Intron|PEG3_ENST00000598410.1_Missense_Mutation_p.R1452H	NM_006210.2	NP_006201.1	Q9GZU2	PEG3_HUMAN	paternally expressed 3	1576			R -> H (in dbSNP:rs34051133).|R -> L. {ECO:0000269|PubMed:11677152}.		apoptotic process (GO:0006915)|genetic imprinting (GO:0071514)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)	p.R1576H(2)		NS(1)|biliary_tract(4)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(27)|lung(84)|ovary(8)|pancreas(5)|prostate(6)|skin(8)|stomach(2)|upper_aerodigestive_tract(6)	170		Colorectal(82;0.000256)|all_neural(62;0.103)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0269)		GAGGGACAGGCGGTCATTGAA	0.527													C|||	908	0.18131	0.0257	0.1758	5008	,	,		20226	0.3948		0.1262	False		,,,				2504	0.2321				p.R1576H		Atlas-SNP	.											ZIM2_ENST00000326441,colon,carcinoma,-1,4	PEG3	414	4	2	Substitution - Missense(2)	stomach(2)	c.G4727A						PASS	.	C	HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,,,HIS/ARG,	204,4202	125.7+/-162.9	4,196,2003	105.0	92.0	96.0		4727,4349,4727,4355,,,4727,	0.5	0.9	19	dbSNP_126	96	1119,7481	231.2+/-265.3	77,965,3258	yes	missense,missense,missense,missense,intron,intron,missense,intron	PEG3,ZIM2	NM_001146184.1,NM_001146185.1,NM_001146186.1,NM_001146187.1,NM_001146326.1,NM_001146327.1,NM_006210.2,NM_015363.4	29,29,29,29,,,29,	81,1161,5261	TT,TC,CC		13.0116,4.63,10.1722	probably-damaging,probably-damaging,probably-damaging,probably-damaging,,,probably-damaging,	1576/1589,1450/1463,1576/1589,1452/1465,,,1576/1589,	57325083	1323,11683	2203	4300	6503	SO:0001583	missense	5178	exon9			GACAGGCGGTCAT	AB006625	CCDS12948.1, CCDS58684.1, CCDS58685.1	19q13.4	2013-01-09				ENSG00000198300		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	8826	protein-coding gene	gene with protein product		601483				9149948	Standard	NM_006210		Approved	ZKSCAN22, KIAA0287, ZNF904, ZSCAN24	uc010etr.2	Q9GZU2		ENST00000326441.9:c.4727G>A	19.37:g.57325083C>T	ENSP00000326581:p.Arg1576His	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	125	11	0.088	NM_001146184	A7E2B8|B4DIM4|C9JP50|P78418|Q5H9P9|Q7Z7H7|Q8TF75|Q9GZY2	Missense_Mutation	SNP	ENST00000326441.9	37	CCDS12948.1	368	0.1684981684981685	11	0.022357723577235773	61	0.1685082872928177	202	0.3531468531468531	94	0.12401055408970976	C	15.05	2.718073	0.48622	0.0463	0.130116	ENSG00000198300	ENST00000326441;ENST00000423103	T;T	0.53206	0.63;0.63	3.87	0.537	0.17144	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.518734	0.16408	N	0.215754	T	0.00012	0.0000	L	0.39633	1.23	.	.	.	B;B;B	0.21753	0.06;0.033;0.06	B;B;B	0.17722	0.019;0.013;0.013	T	0.36311	-0.9753	9	0.32370	T	0.25	-9.655	3.157	0.06508	0.2103:0.5647:0.0:0.225	rs34051133	1452;1576;1511	A7E2B8;Q9GZU2;Q96Q96	.;PEG3_HUMAN;.	H	1576	ENSP00000326581:R1576H;ENSP00000403051:R1576H	ENSP00000326581:R1576H	R	-	2	0	ZIM2	62016895	0.000000	0.05858	0.879000	0.34478	0.646000	0.38490	-0.283000	0.08433	0.216000	0.20781	-0.293000	0.09583	CGC	C|0.872;T|0.128	0.128	strong		0.527	PEG3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416099.2		
FSIP2	401024	hgsc.bcm.edu	37	2	186672897	186672897	+	Silent	SNP	A	A	G	rs4666690	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr2:186672897A>G	ENST00000424728.1	+	17	18864	c.18864A>G	c.(18862-18864)ttA>ttG	p.L6288L	FSIP2_ENST00000343098.5_Silent_p.L6377L			Q5CZC0	FSIP2_HUMAN	fibrous sheath interacting protein 2	6288										NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(4)|kidney(1)|large_intestine(11)|lung(46)|pancreas(1)|urinary_tract(2)	69						TAGGCTTTTTAATGGTGAATG	0.323													A|||	1637	0.326877	0.2451	0.3559	5008	,	,		17961	0.4077		0.3658	False		,,,				2504	0.2935				p.L6377L		Atlas-SNP	.											FSIP2_ENST00000343098,caecum,carcinoma,+2,2	FSIP2	251	2	0			c.A19131G						scavenged	.	A		874,2742		97,680,1031	46.0	43.0	44.0		19131	3.3	1.0	2	dbSNP_111	44	2881,5255		502,1877,1689	no	coding-synonymous	FSIP2	NM_173651.2		599,2557,2720	GG,GA,AA		35.4105,24.1704,31.952		6377/6997	186672897	3755,7997	1808	4068	5876	SO:0001819	synonymous_variant	401024	exon17			CTTTTTAATGGTG	AK092099	CCDS54426.1	2q32.1	2010-06-18			ENSG00000188738	ENSG00000188738			21675	protein-coding gene	gene with protein product		615796				14702039	Standard	NM_173651		Approved	FLJ34780	uc002upl.3	Q5CZC0	OTTHUMG00000153874	ENST00000424728.1:c.18864A>G	2.37:g.186672897A>G		Somatic	433	0	0		WXS	Illumina HiSeq	Phase_I	415	10	0.0240964	NM_173651	Q53TL3|Q53TN5|Q5HYH2|Q6ZTZ5|Q6ZU14|Q6ZU21	Silent	SNP	ENST00000424728.1	37																																																																																				A|0.658;G|0.342	0.342	strong		0.323	FSIP2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000332778.3	NM_173651	
CFHR2	3080	hgsc.bcm.edu	37	1	196884258	196884258	+	Intron	SNP	A	A	T	rs150845796		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr1:196884258A>T	ENST00000367421.3	+	2	135				CFHR4_ENST00000367418.2_Silent_p.P263P|CFHR4_ENST00000608469.1_Silent_p.P133P|CFHR4_ENST00000251424.4_Silent_p.P263P|CFHR4_ENST00000367416.2_Silent_p.P509P			P36980	FHR2_HUMAN	complement factor H-related 2							extracellular region (GO:0005576)				large_intestine(2)|ovary(1)|skin(3)	6						CGGAACCACCAAGATGCATAC	0.358																																					p.P510P		Atlas-SNP	.											CFHR4_ENST00000367416,right_lower_lobe,carcinoma,+1,2	CFHR4	141	2	0			c.A1530T						scavenged	.						67.0	69.0	68.0					1																	196884258		2199	4295	6494	SO:0001627	intron_variant	10877	exon9			ACCACCAAGATGC	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	ENST00000367421.3:c.59-34327A>T	1.37:g.196884258A>T		Somatic	733	2	0.00272851		WXS	Illumina HiSeq	Phase_I	890	13	0.0146067	NM_001201550	Q14310|Q5T9T1	Silent	SNP	ENST00000367421.3	37																																																																																				.	.	weak		0.358	CFHR2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_005666	
TRIM51	84767	hgsc.bcm.edu	37	11	55655597	55655597	+	Silent	SNP	A	A	G			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr11:55655597A>G	ENST00000449290.2	+	4	689	c.597A>G	c.(595-597)gaA>gaG	p.E199E	TRIM51_ENST00000244891.3_Silent_p.E56E	NM_032681.3	NP_116070.2	Q9BSJ1	TRI51_HUMAN	tripartite motif-containing 51	199						intracellular (GO:0005622)	zinc ion binding (GO:0008270)										ATCACTTGGAAAGGCTGCGAA	0.433																																					p.E199E		Atlas-SNP	.											SPRYD5_ENST00000327733,NS,carcinoma,+2,2	.	.	2	0			c.A597G						scavenged	.						61.0	58.0	59.0					11																	55655597		2201	4296	6497	SO:0001819	synonymous_variant	84767	exon4			CTTGGAAAGGCTG	BC005014		11p11	2013-01-09	2012-05-18	2012-05-18	ENSG00000124900	ENSG00000124900		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	19023	protein-coding gene	gene with protein product			"""SPRY domain containing 5"""	SPRYD5			Standard	NM_032681		Approved	TRIM51A	uc010rip.2	Q9BSJ1	OTTHUMG00000156437	ENST00000449290.2:c.597A>G	11.37:g.55655597A>G		Somatic	599	41	0.0684474		WXS	Illumina HiSeq	Phase_I	580	27	0.0465517	NM_032681	A6NMG2	Silent	SNP	ENST00000449290.2	37																																																																																				.	.	none		0.433	TRIM51-004	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000391522.1	NM_032681	
TTN	7273	hgsc.bcm.edu	37	2	179579822	179579822	+	Silent	SNP	T	T	A	rs2562836	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr2:179579822T>A	ENST00000591111.1	-	88	25364	c.25140A>T	c.(25138-25140)ctA>ctT	p.L8380L	TTN_ENST00000460472.2_Intron|TTN_ENST00000589042.1_Silent_p.L8697L|TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000431752.1_RNA|TTN_ENST00000342992.6_Silent_p.L7453L|TTN_ENST00000359218.5_Intron|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342175.6_Intron			Q8WZ42	TITIN_HUMAN	titin	12554	Ig-like 66.				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)			GGATACTGGTTAGGAAGTTCT	0.463													A|||	2226	0.444489	0.4644	0.379	5008	,	,		20441	0.6577		0.2237	False		,,,				2504	0.4714				p.L8697L		Atlas-SNP	.											.	TTN	18412	.	0			c.A26091T						PASS	.	A	,,,	1560,2344		323,914,715	314.0	300.0	305.0		,22359,,	-4.7	0.0	2	dbSNP_100	305	1660,6618		160,1340,2639	no	intron,coding-synonymous,intron,intron	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	,,,	483,2254,3354	AA,AT,TT		20.0532,39.959,26.4324	,,,	,7453/33424,,	179579822	3220,8962	1952	4139	6091	SO:0001819	synonymous_variant	7273	exon90			ACTGGTTAGGAAG	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.25140A>T	2.37:g.179579822T>A		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	115	9	0.0782609	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|0.630;N|0.001	.	strong		0.463	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
RELN	5649	hgsc.bcm.edu	37	7	103474041	103474041	+	Missense_Mutation	SNP	G	G	C	rs79471015	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr7:103474041G>C	ENST00000428762.1	-	3	575	c.416C>G	c.(415-417)aCc>aGc	p.T139S	RELN_ENST00000343529.5_Missense_Mutation_p.T139S|RELN_ENST00000424685.2_Missense_Mutation_p.T139S	NM_005045.3	NP_005036.2	P78509	RELN_HUMAN	reelin	139	Reelin. {ECO:0000255|PROSITE- ProRule:PRU00363}.				associative learning (GO:0008306)|axon guidance (GO:0007411)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cell morphogenesis involved in differentiation (GO:0000904)|central nervous system development (GO:0007417)|cerebral cortex tangential migration (GO:0021800)|dendrite development (GO:0016358)|glial cell differentiation (GO:0010001)|hippocampus development (GO:0021766)|lateral motor column neuron migration (GO:0097477)|layer formation in cerebral cortex (GO:0021819)|long-term memory (GO:0007616)|N-methyl-D-aspartate receptor clustering (GO:0097114)|neuron migration (GO:0001764)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000969)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of lateral motor column neuron migration (GO:1902078)|positive regulation of long-term synaptic potentiation (GO:1900273)|positive regulation of neuron projection development (GO:0010976)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of TOR signaling (GO:0032008)|postsynaptic density protein 95 clustering (GO:0097119)|receptor localization to synapse (GO:0097120)|reelin-mediated signaling pathway (GO:0038026)|regulation of behavior (GO:0050795)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of synaptic transmission (GO:0050804)|response to pain (GO:0048265)|spinal cord patterning (GO:0021511)|ventral spinal cord development (GO:0021517)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	lipoprotein particle receptor binding (GO:0070325)|metal ion binding (GO:0046872)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|serine-type peptidase activity (GO:0008236)|very-low-density lipoprotein particle receptor binding (GO:0070326)			NS(3)|breast(8)|central_nervous_system(3)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|lung(101)|ovary(9)|pancreas(2)|prostate(4)|skin(14)|stomach(2)|upper_aerodigestive_tract(12)|urinary_tract(2)	227				COAD - Colon adenocarcinoma(1;8.98e-05)|Colorectal(1;0.00184)		ACTGAGGTTGGTTGTGGGCAG	0.488													G|||	86	0.0171725	0.0	0.0159	5008	,	,		16300	0.0734		0.0	False		,,,				2504	0.001				p.T139S	NSCLC(146;835 1944 15585 22231 52158)	Atlas-SNP	.											.	RELN	593	.	0			c.C416G						PASS	.	G	SER/THR,SER/THR	3,4403	6.2+/-15.9	0,3,2200	122.0	107.0	112.0		416,416	5.3	1.0	7	dbSNP_131	112	4,8596	3.7+/-12.6	0,4,4296	yes	missense,missense	RELN	NM_005045.3,NM_173054.2	58,58	0,7,6496	CC,CG,GG		0.0465,0.0681,0.0538	benign,benign	139/3461,139/3459	103474041	7,12999	2203	4300	6503	SO:0001583	missense	5649	exon3			AGGTTGGTTGTGG		CCDS34722.1, CCDS47680.1	7q22	2008-07-18			ENSG00000189056	ENSG00000189056			9957	protein-coding gene	gene with protein product		600514				9049633	Standard	NM_005045		Approved	RL, PRO1598	uc010liz.3	P78509	OTTHUMG00000157247	ENST00000428762.1:c.416C>G	7.37:g.103474041G>C	ENSP00000392423:p.Thr139Ser	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	110	7	0.0636364	NM_173054	A4D0P9|A4D0Q0|Q86UJ0|Q86UJ8|Q8NDV0|Q9UDQ2	Missense_Mutation	SNP	ENST00000428762.1	37	CCDS47680.1	52	0.023809523809523808	0	0.0	5	0.013812154696132596	47	0.08216783216783216	0	0.0	G	14.71	2.617974	0.46736	6.81E-4	4.65E-4	ENSG00000189056	ENST00000428762;ENST00000343529;ENST00000424685;ENST00000448171	T;T;T	0.24350	1.86;1.86;1.86	5.33	5.33	0.75918	Reeler domain (2);	0.115168	0.56097	D	0.000024	T	0.00875	0.0029	N	0.11560	0.145	0.42964	D	0.994417	B;B	0.22746	0.06;0.074	B;B	0.27887	0.05;0.084	T	0.13575	-1.0504	10	0.27785	T	0.31	.	19.3931	0.94592	0.0:0.0:1.0:0.0	.	139;139	P78509-2;P78509	.;RELN_HUMAN	S	139	ENSP00000392423:T139S;ENSP00000345694:T139S;ENSP00000388446:T139S	ENSP00000345694:T139S	T	-	2	0	RELN	103261277	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.617000	0.67716	2.634000	0.89283	0.650000	0.86243	ACC	G|0.993;C|0.007	0.007	strong		0.488	RELN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348148.1	NM_005045	
RASSF8	11228	hgsc.bcm.edu	37	12	26218197	26218197	+	Silent	SNP	G	G	A	rs79553120	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr12:26218197G>A	ENST00000405154.2	+	3	1069	c.870G>A	c.(868-870)gaG>gaA	p.E290E	RASSF8_ENST00000282884.9_Silent_p.E290E|RASSF8_ENST00000541490.1_Silent_p.E290E|RASSF8_ENST00000381352.3_Silent_p.E290E|RASSF8_ENST00000542865.1_Silent_p.E290E	NM_001164748.1	NP_001158220.1	Q8NHQ8	RASF8_HUMAN	Ras association (RalGDS/AF-6) domain family (N-terminal) member 8	290	Glu-rich.				signal transduction (GO:0007165)					cervix(2)|endometrium(1)|large_intestine(6)|lung(15)|urinary_tract(1)	25	Colorectal(261;0.0847)					ATGAGGAAGAGGTTAAAGGAA	0.443													G|||	38	0.00758786	0.0	0.0	5008	,	,		20063	0.0317		0.0	False		,,,				2504	0.0061				p.E290E		Atlas-SNP	.											RASSF8_ENST00000541490,right_lower_lobe,carcinoma,+2,4	RASSF8	56	4	0			c.G870A						scavenged	.						114.0	106.0	109.0					12																	26218197		2203	4300	6503	SO:0001819	synonymous_variant	11228	exon4			GGAAGAGGTTAAA	U82396	CCDS8705.1, CCDS53765.1	12p12.3	2013-05-30	2008-02-22	2005-09-14	ENSG00000123094	ENSG00000123094			13232	protein-coding gene	gene with protein product		608231	"""chromosome 12 open reading frame 2"""	C12orf2			Standard	NM_007211		Approved	HoJ-1	uc001rgx.3	Q8NHQ8	OTTHUMG00000169087	ENST00000405154.2:c.870G>A	12.37:g.26218197G>A		Somatic	258	0	0		WXS	Illumina HiSeq	Phase_I	269	8	0.0297398	NM_007211	A8K1Z0|O95647|Q5SCI2|Q76KB6	Silent	SNP	ENST00000405154.2	37	CCDS53765.1																																																																																			G|0.992;A|0.008	0.008	strong		0.443	RASSF8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402209.2	NM_007211	
FRMD6	122786	hgsc.bcm.edu	37	14	52156605	52156605	+	Silent	SNP	T	T	C			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr14:52156605T>C	ENST00000344768.5	+	2	247	c.51T>C	c.(49-51)agT>agC	p.S17S	FRMD6_ENST00000356218.4_Silent_p.S17S|FRMD6_ENST00000395718.2_Silent_p.S17S|RNA5SP385_ENST00000515947.1_RNA			Q96NE9	FRMD6_HUMAN	FERM domain containing 6	17	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				apical constriction (GO:0003383)|cellular protein localization (GO:0034613)|regulation of actin filament-based process (GO:0032970)	apical junction complex (GO:0043296)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|endometrium(7)|large_intestine(7)|lung(11)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34	all_epithelial(31;0.0163)|Breast(41;0.089)					ACCGCCGCAGTGTGTGCATTT	0.433																																					p.S17S		Atlas-SNP	.											FRMD6,NS,carcinoma,+1,2	FRMD6	100	2	0			c.T51C						scavenged	.						107.0	89.0	95.0					14																	52156605		2203	4300	6503	SO:0001819	synonymous_variant	122786	exon2			CCGCAGTGTGTGC	BI465118	CCDS9704.1, CCDS58318.1, CCDS58319.1	14q22.1	2011-06-22	2005-07-20	2005-07-20	ENSG00000139926	ENSG00000139926			19839	protein-coding gene	gene with protein product	"""expanded homolog"""	614555	"""chromosome 14 open reading frame 31"""	C14orf31			Standard	NM_152330		Approved	MGC17921, willin, EX1	uc001wzd.3	Q96NE9	OTTHUMG00000140294	ENST00000344768.5:c.51T>C	14.37:g.52156605T>C		Somatic	246	3	0.0121951		WXS	Illumina HiSeq	Phase_I	246	7	0.0284553	NM_001267046	D3DSB9|Q5HYF2|Q8N2X1|Q8WUH7	Silent	SNP	ENST00000344768.5	37	CCDS58318.1																																																																																			.	.	none		0.433	FRMD6-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000276881.1	NM_152330	
SACS	26278	hgsc.bcm.edu	37	13	23929842	23929842	+	Silent	SNP	T	T	C	rs41315020	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr13:23929842T>C	ENST00000382292.3	-	7	1182	c.909A>G	c.(907-909)gcA>gcG	p.A303A	SACS_ENST00000382298.3_Silent_p.A303A|SACS_ENST00000402364.1_5'UTR|SACS_ENST00000476776.1_5'Flank			Q9NZJ4	SACS_HUMAN	sacsin molecular chaperone	303					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)	p.A156A(1)		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)		GCACTGTGTCTGCATCTGCCC	0.443													T|||	255	0.0509185	0.0113	0.0288	5008	,	,		20441	0.1627		0.0378	False		,,,				2504	0.0184				p.A303A		Atlas-SNP	.											SACS,NS,carcinoma,0,1	SACS	871	1	1	Substitution - coding silent(1)	stomach(1)	c.A909G						scavenged	.	T		104,4302	81.9+/-120.4	0,104,2099	97.0	96.0	96.0		909	-7.7	0.8	13	dbSNP_127	96	364,8236	121.3+/-180.4	3,358,3939	no	coding-synonymous	SACS	NM_014363.4		3,462,6038	CC,CT,TT		4.2326,2.3604,3.5983		303/4580	23929842	468,12538	2203	4300	6503	SO:0001819	synonymous_variant	26278	exon8			TGTGTCTGCATCT	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.909A>G	13.37:g.23929842T>C		Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	175	6	0.0342857	NM_014363	O94835|Q5T9J5|Q5T9J7|Q5T9J8|Q68DF5|Q6MZR4|Q8NBF9	Silent	SNP	ENST00000382292.3	37	CCDS9300.2	129	0.059065934065934064	11	0.022357723577235773	12	0.03314917127071823	77	0.1346153846153846	29	0.03825857519788918	T	10.28	1.306139	0.23736	0.023604	0.042326	ENSG00000151835	ENST00000455470	.	.	.	5.86	-7.73	0.01245	.	.	.	.	.	T	0.00109	0.0003	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.25745	-1.0123	3	.	.	.	.	0.0814	0.00032	0.2669:0.2137:0.1838:0.3356	rs41315020;rs57420292;rs61736775	.	.	.	G	203	.	.	R	-	1	2	SACS	22827842	0.023000	0.18921	0.775000	0.31657	0.974000	0.67602	-0.897000	0.04110	-1.501000	0.01817	-0.309000	0.09137	AGA	T|0.956;C|0.044	0.044	strong		0.443	SACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044148.3	NM_014363	
ST6GAL2	84620	hgsc.bcm.edu	37	2	107459974	107459974	+	Missense_Mutation	SNP	C	C	T	rs3796110	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr2:107459974C>T	ENST00000409382.3	-	2	1070	c.460G>A	c.(460-462)Ggg>Agg	p.G154R	AC016994.2_ENST00000425419.1_RNA|ST6GAL2_ENST00000361686.4_Missense_Mutation_p.G154R|ST6GAL2_ENST00000409087.3_Missense_Mutation_p.G154R	NM_001142351.1	NP_001135823.1	Q96JF0	SIAT2_HUMAN	ST6 beta-galactosamide alpha-2,6-sialyltranferase 2	154			G -> R (in dbSNP:rs3796110).		growth (GO:0040007)|multicellular organismal development (GO:0007275)|oligosaccharide metabolic process (GO:0009311)|protein glycosylation (GO:0006486)|sialylation (GO:0097503)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	beta-galactoside alpha-2,6-sialyltransferase activity (GO:0003835)			autonomic_ganglia(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(8)|liver(1)|lung(30)|ovary(5)|pancreas(6)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	65						CCTGGCTCCCCGGGGGAAGGG	0.617													C|||	702	0.140176	0.1505	0.147	5008	,	,		14211	0.1369		0.1014	False		,,,				2504	0.1646				p.G154R		Atlas-SNP	.											ST6GAL2,NS,carcinoma,+1,1	ST6GAL2	159	1	0			c.G460A						PASS	.	C	ARG/GLY,ARG/GLY,ARG/GLY	655,3751	268.3+/-268.4	41,573,1589	82.0	99.0	93.0		460,460,460	-2.2	0.0	2	dbSNP_107	93	639,7961	160.4+/-213.5	20,599,3681	yes	missense,missense,missense	ST6GAL2	NM_001142351.1,NM_001142352.1,NM_032528.2	125,125,125	61,1172,5270	TT,TC,CC		7.4302,14.8661,9.9493	benign,benign,benign	154/530,154/467,154/530	107459974	1294,11712	2203	4300	6503	SO:0001583	missense	84620	exon2			GCTCCCCGGGGGA	AB059555	CCDS2073.1, CCDS46380.1	2q11-q12	2008-02-05	2005-02-07	2005-02-07	ENSG00000144057	ENSG00000144057	2.4.99.2		10861	protein-coding gene	gene with protein product		608472	"""sialyltransferase 2 (monosialoganglioside sialyltransferase)"""	SIAT2			Standard	NM_032528		Approved	KIAA1877, St6gal2, St6GalII	uc002tdr.3	Q96JF0	OTTHUMG00000130923	ENST00000409382.3:c.460G>A	2.37:g.107459974C>T	ENSP00000386942:p.Gly154Arg	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	112	7	0.0625	NM_032528	D3DVK3|Q53QP4|Q86Y44|Q8IUG7|Q96HE4	Missense_Mutation	SNP	ENST00000409382.3	37	CCDS2073.1	263	0.12042124542124542	73	0.1483739837398374	41	0.1132596685082873	73	0.12762237762237763	76	0.10026385224274406	C	4.589	0.109487	0.08780	0.148661	0.074302	ENSG00000144057	ENST00000361686;ENST00000409382;ENST00000409087	T;T;T	0.30981	2.53;2.53;1.51	4.89	-2.16	0.07080	.	1.084480	0.07015	N	0.825771	T	0.00073	0.0002	N	0.08118	0	0.80722	P	0.0	B;B	0.21381	0.055;0.01	B;B	0.10450	0.005;0.003	T	0.37911	-0.9685	9	0.13470	T	0.59	-3.3377	13.0284	0.58829	0.0:0.4981:0.0:0.5019	rs3796110;rs61140784;rs3796110	154;154	Q96JF0-2;Q96JF0	.;SIAT2_HUMAN	R	154	ENSP00000355273:G154R;ENSP00000386942:G154R;ENSP00000387332:G154R	ENSP00000355273:G154R	G	-	1	0	ST6GAL2	106826406	0.000000	0.05858	0.000000	0.03702	0.165000	0.22458	-1.227000	0.02950	-0.671000	0.05274	-1.134000	0.01955	GGG	C|0.893;T|0.107	0.107	strong		0.617	ST6GAL2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330065.1	NM_032528	
MUC4	4585	hgsc.bcm.edu	37	3	195506005	195506005	+	Missense_Mutation	SNP	A	A	C	rs202017381	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr3:195506005A>C	ENST00000463781.3	-	2	12905	c.12446T>G	c.(12445-12447)aTc>aGc	p.I4149S	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.I4149S	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.I4149S(2)		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)		TGAGGAAGGGATGGTGACAGG	0.587													.|||	15	0.00299521	0.0076	0.0	5008	,	,		11242	0.0		0.001	False		,,,				2504	0.0041				p.I4149S		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	2	Substitution - Missense(2)	kidney(1)|endometrium(1)	c.T12446G						scavenged	.						41.0	23.0	28.0					3																	195506005		646	1562	2208	SO:0001583	missense	4585	exon2			GAAGGGATGGTGA	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.12446T>G	3.37:g.195506005A>C	ENSP00000417498:p.Ile4149Ser	Somatic	33	7	0.212121		WXS	Illumina HiSeq	Phase_I	30	7	0.233333	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	0.001	-3.494649	0.00010	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.36157	1.3;1.27	.	.	.	.	.	.	.	.	T	0.10208	0.0250	N	0.08118	0	0.09310	N	1	B	0.31931	0.347	B	0.20577	0.03	T	0.06552	-1.0820	7	.	.	.	.	2.1553	0.03810	0.4926:0.2533:0.0:0.254	.	4021	E7ESK3	.	S	4149	ENSP00000417498:I4149S;ENSP00000420243:I4149S	.	I	-	2	0	MUC4	196990784	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.259000	0.18405	-4.179000	0.00067	-4.128000	0.00010	ATC	.	.	weak		0.587	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
RSPH3	83861	hgsc.bcm.edu	37	6	159407446	159407446	+	Missense_Mutation	SNP	C	C	T	rs34582178	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr6:159407446C>T	ENST00000252655.1	-	3	827	c.638G>A	c.(637-639)cGg>cAg	p.R213Q	RSPH3_ENST00000449822.1_Intron|RP1-111C20.4_ENST00000607391.1_RNA|RSPH3_ENST00000367069.2_Missense_Mutation_p.R71Q|RSPH3_ENST00000297262.3_Intron	NM_031924.4	NP_114130.3	Q86UC2	RSPH3_HUMAN	radial spoke 3 homolog (Chlamydomonas)	213			R -> Q (in dbSNP:rs34582178).					p.R213Q(1)		endometrium(3)|kidney(2)|large_intestine(1)|lung(7)|ovary(2)|skin(1)|stomach(7)	23		Breast(66;0.00519)|Ovarian(120;0.123)		OV - Ovarian serous cystadenocarcinoma(65;2.36e-16)|BRCA - Breast invasive adenocarcinoma(81;5.92e-06)		AGAATCAGGCCGTCCGAGCTA	0.433													T|||	1064	0.21246	0.0651	0.3746	5008	,	,		17667	0.3919		0.1034	False		,,,				2504	0.2239				p.R213Q		Atlas-SNP	.											RSPH3,NS,carcinoma,0,1	RSPH3	48	1	1	Substitution - Missense(1)	stomach(1)	c.G638A						PASS	.	T	GLN/ARG	404,4002	788.9+/-415.0	12,380,1811	173.0	150.0	158.0		638	4.5	0.9	6	dbSNP_126	158	926,7674	777.0+/-407.7	61,804,3435	yes	missense	RSPH3	NM_031924.4	43	73,1184,5246	TT,TC,CC		10.7674,9.1693,10.226	benign	213/561	159407446	1330,11676	2203	4300	6503	SO:0001583	missense	83861	exon3			TCAGGCCGTCCGA	AF353618	CCDS5260.1	6q25.3	2014-05-16	2008-07-04	2007-06-26	ENSG00000130363	ENSG00000130363			21054	protein-coding gene	gene with protein product		615876	"""radial spokehead-like 2"""	RSHL2		12477932	Standard	NM_031924		Approved	dJ111C20.1, RSP3	uc003qrx.3	Q86UC2	OTTHUMG00000015924	ENST00000252655.1:c.638G>A	6.37:g.159407446C>T	ENSP00000252655:p.Arg213Gln	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	73	4	0.0547945	NM_031924	Q96LQ5|Q96LX2|Q9BX75	Missense_Mutation	SNP	ENST00000252655.1	37	CCDS5260.1	469	0.21474358974358973	33	0.06707317073170732	109	0.3011049723756906	244	0.42657342657342656	83	0.10949868073878628	T	1.013	-0.687310	0.03328	0.091693	0.107674	ENSG00000130363	ENST00000367069;ENST00000252655	T;T	0.15952	2.38;2.38	5.64	4.47	0.54385	.	0.266353	0.37483	N	0.002061	T	0.00906	0.0030	N	0.00280	-1.71	0.09310	P	0.9999999999999999	B	0.06786	0.001	B	0.04013	0.001	T	0.46442	-0.9191	9	0.02654	T	1	-22.7582	9.8258	0.40910	0.0:0.1457:0.0:0.8543	rs34582178	213	Q86UC2	RSPH3_HUMAN	Q	71;213	ENSP00000356036:R71Q;ENSP00000252655:R213Q	ENSP00000252655:R213Q	R	-	2	0	RSPH3	159327434	1.000000	0.71417	0.862000	0.33874	0.024000	0.10985	2.353000	0.44089	0.981000	0.38548	-0.269000	0.10298	CGG	C|0.861;T|0.139	0.139	strong		0.433	RSPH3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_031924	
KLHL6	89857	hgsc.bcm.edu	37	3	183226186	183226186	+	Silent	SNP	C	C	T	rs61447052	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr3:183226186C>T	ENST00000341319.3	-	3	605	c.570G>A	c.(568-570)aaG>aaA	p.K190K		NM_130446.2	NP_569713.2	Q8WZ60	KLHL6_HUMAN	kelch-like family member 6	190	BACK.				B cell receptor signaling pathway (GO:0050853)|germinal center formation (GO:0002467)			p.K190K(1)		breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(7)|kidney(1)|large_intestine(6)|liver(1)|lung(16)|ovary(2)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	44	all_cancers(143;9.2e-12)|Ovarian(172;0.0172)		all cancers(12;1.29e-44)|Epithelial(37;1.24e-38)|LUSC - Lung squamous cell carcinoma(7;2.58e-24)|Lung(8;1.79e-22)|OV - Ovarian serous cystadenocarcinoma(80;2.32e-22)			GAACCTGCTTCTTTAGACTGT	0.493													C|||	403	0.0804712	0.0908	0.0303	5008	,	,		20474	0.1786		0.001	False		,,,				2504	0.0828				p.K190K		Atlas-SNP	.											KLHL6,NS,carcinoma,0,1	KLHL6	100	1	1	Substitution - coding silent(1)	stomach(1)	c.G570A						scavenged	.	C		323,4083	171.2+/-201.5	9,305,1889	71.0	75.0	73.0		570	5.0	1.0	3	dbSNP_129	73	7,8593	6.4+/-24.3	0,7,4293	no	coding-synonymous	KLHL6	NM_130446.2		9,312,6182	TT,TC,CC		0.0814,7.3309,2.5373		190/622	183226186	330,12676	2203	4300	6503	SO:0001819	synonymous_variant	89857	exon3			CTGCTTCTTTAGA	AF441792	CCDS3245.2	3q27.3	2013-01-30	2013-01-30		ENSG00000172578	ENSG00000172578		"""Kelch-like"", ""BTB/POZ domain containing"""	18653	protein-coding gene	gene with protein product	"""kelch-like protein KLHL6"""	614214	"""kelch-like 6 (Drosophila)"""			11214971, 12617994	Standard	NM_130446		Approved	FLJ00029	uc003flr.3	Q8WZ60	OTTHUMG00000148673	ENST00000341319.3:c.570G>A	3.37:g.183226186C>T		Somatic	94	1	0.0106383		WXS	Illumina HiSeq	Phase_I	90	6	0.0666667	NM_130446	B2RB31|D3DNS8|Q8N5I1|Q8N892	Silent	SNP	ENST00000341319.3	37	CCDS3245.2																																																																																			C|0.963;T|0.037	0.037	strong		0.493	KLHL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309024.1	NM_130446	
GPR98	84059	hgsc.bcm.edu	37	5	90151589	90151589	+	Missense_Mutation	SNP	G	G	A	rs2247870	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr5:90151589G>A	ENST00000405460.2	+	82	17722	c.17626G>A	c.(17626-17628)Gtt>Att	p.V5876I	GPR98_ENST00000425867.2_Missense_Mutation_p.V1537I	NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	5876	GPS. {ECO:0000255|PROSITE- ProRule:PRU00098}.			V -> I (in Ref. 1; AAD55586, 2; AAL30811 and 6; BAA31661). {ECO:0000305}.	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)	p.V5876I(1)		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)		TTGCAAAGTGGTTGAGGAAAC	0.413													G|||	2299	0.459065	0.1309	0.6931	5008	,	,		20690	0.5665		0.5606	False		,,,				2504	0.5215				p.V5876I		Atlas-SNP	.											GPR98,NS,carcinoma,0,1	GPR98	605	1	1	Substitution - Missense(1)	stomach(1)	c.G17626A						PASS	.	G	ILE/VAL	759,3129		70,619,1255	297.0	274.0	281.0		17626	4.6	1.0	5	dbSNP_100	281	4531,3749		1235,2061,844	yes	missense	GPR98	NM_032119.3	29	1305,2680,2099	AA,AG,GG		45.2778,19.5216,43.4747	benign	5876/6307	90151589	5290,6878	1944	4140	6084	SO:0001583	missense	84059	exon82			AAAGTGGTTGAGG	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.17626G>A	5.37:g.90151589G>A	ENSP00000384582:p.Val5876Ile	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	122	5	0.0409836	NM_032119	O75171|Q8TF58|Q9H0X5|Q9UL61	Missense_Mutation	SNP	ENST00000405460.2	37	CCDS47246.1	1082	0.49542124542124544	72	0.14634146341463414	244	0.6740331491712708	334	0.583916083916084	432	0.5699208443271768	G	12.62	1.991585	0.35131	0.195216	0.547222	ENSG00000164199	ENST00000405460;ENST00000296619;ENST00000425867	T;T	0.70164	-0.46;-0.46	5.5	4.64	0.57946	GPS domain (3);	0.111041	0.64402	D	0.000012	T	0.00012	0.0000	L	0.41710	1.295	0.20403	P	0.9999025175	B;P;B	0.36974	0.012;0.576;0.01	B;B;B	0.34242	0.016;0.178;0.009	T	0.46857	-0.9161	8	.	.	.	.	11.3472	0.49567	0.1921:0.0:0.8079:0.0	rs2247870;rs56587026;rs60466685;rs2247870	1537;5876;1537	E7EML1;Q8WXG9;Q8WXG9-2	.;GPR98_HUMAN;.	I	5876;5876;1537	ENSP00000384582:V5876I;ENSP00000392618:V1537I	.	V	+	1	0	GPR98	90187345	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	2.899000	0.48679	1.465000	0.48006	-0.216000	0.12614	GTT	G|0.534;A|0.466	0.466	strong		0.413	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119	
STAB1	23166	hgsc.bcm.edu	37	3	52548818	52548818	+	Silent	SNP	C	C	T	rs740903	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr3:52548818C>T	ENST00000321725.6	+	35	3856	c.3780C>T	c.(3778-3780)tgC>tgT	p.C1260C		NM_015136.2	NP_055951.2	Q9NY15	STAB1_HUMAN	stabilin 1	1260					cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|defense response to bacterium (GO:0042742)|inflammatory response (GO:0006954)|negative regulation of angiogenesis (GO:0016525)|oxidation-reduction process (GO:0055114)|receptor-mediated endocytosis (GO:0006898)	endocytic vesicle membrane (GO:0030666)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	hyaluronic acid binding (GO:0005540)|low-density lipoprotein particle binding (GO:0030169)|low-density lipoprotein receptor activity (GO:0005041)|protein disulfide oxidoreductase activity (GO:0015035)|scavenger receptor activity (GO:0005044)			breast(4)|central_nervous_system(3)|endometrium(7)|kidney(2)|large_intestine(13)|liver(1)|lung(27)|ovary(1)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(3)	76				BRCA - Breast invasive adenocarcinoma(193;1.73e-05)|Kidney(197;0.00182)|KIRC - Kidney renal clear cell carcinoma(197;0.00205)|OV - Ovarian serous cystadenocarcinoma(275;0.0482)		CAAGTCGCTGCCTGCATAGCC	0.667													C|||	821	0.163938	0.0461	0.1412	5008	,	,		17171	0.2331		0.0934	False		,,,				2504	0.3405				p.C1260C		Atlas-SNP	.											.	STAB1	178	.	0			c.C3780T						PASS	.	C		298,4108	158.5+/-191.2	11,276,1916	42.0	46.0	45.0		3780	2.5	1.0	3	dbSNP_86	45	975,7625	210.1+/-251.1	53,869,3378	no	coding-synonymous	STAB1	NM_015136.2		64,1145,5294	TT,TC,CC		11.3372,6.7635,9.7878		1260/2571	52548818	1273,11733	2203	4300	6503	SO:0001819	synonymous_variant	23166	exon35			TCGCTGCCTGCAT	AJ275213	CCDS33768.1	3p21.31	2008-07-18			ENSG00000010327	ENSG00000010327			18628	protein-coding gene	gene with protein product	"""MS-1 antigen"", ""fasciclin egf-like, laminin-type egf-like, and link domain-containing scavenger receptor-1"", ""common lymphatic endothelial and vascular endothelial receptor-1"""	608560				11829752, 12077138	Standard	XM_005264973		Approved	KIAA0246, STAB-1, FEEL-1, CLEVER-1, FELE-1, FEX1	uc003dej.3	Q9NY15	OTTHUMG00000158574	ENST00000321725.6:c.3780C>T	3.37:g.52548818C>T		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	52	4	0.0769231	NM_015136	A7E297|Q8IUH0|Q8IUH1|Q93072	Silent	SNP	ENST00000321725.6	37	CCDS33768.1																																																																																			C|0.890;T|0.110	0.110	strong		0.667	STAB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351380.2	NM_015136	
PPARGC1B	133522	hgsc.bcm.edu	37	5	149212510	149212510	+	Missense_Mutation	SNP	C	C	A	rs11959820	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr5:149212510C>A	ENST00000309241.5	+	5	906	c.874C>A	c.(874-876)Cgc>Agc	p.R292S	PPARGC1B_ENST00000360453.4_Missense_Mutation_p.R253S|PPARGC1B_ENST00000394320.3_Missense_Mutation_p.R292S|PPARGC1B_ENST00000403750.1_Missense_Mutation_p.R228S	NM_133263.3	NP_573570.3	Q86YN6	PRGC2_HUMAN	peroxisome proliferator-activated receptor gamma, coactivator 1 beta	292			R -> S (in dbSNP:rs11959820). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:15863669}.		actin filament organization (GO:0007015)|bone trabecula formation (GO:0060346)|cellular lipid metabolic process (GO:0044255)|cellular response to reactive oxygen species (GO:0034614)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of transcription, DNA-templated (GO:0045892)|ossification (GO:0001503)|positive regulation of alkaline phosphatase activity (GO:0010694)|positive regulation of bone resorption (GO:0045780)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of phosphorylation (GO:0042327)|positive regulation of receptor activity (GO:2000273)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to cAMP (GO:0051591)|response to glucocorticoid (GO:0051384)|small molecule metabolic process (GO:0044281)|transcription from mitochondrial promoter (GO:0006390)|transcription from RNA polymerase II promoter (GO:0006366)	mediator complex (GO:0016592)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	AF-2 domain binding (GO:0050682)|estrogen receptor binding (GO:0030331)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nucleotide binding (GO:0000166)|receptor activator activity (GO:0030546)|RNA binding (GO:0003723)|RNA polymerase II transcription cofactor activity (GO:0001104)			NS(1)|breast(1)|endometrium(1)|kidney(3)|large_intestine(1)|liver(2)|lung(15)|ovary(3)|prostate(2)|stomach(1)	30			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)			GCAACTCATACGCTACATGCA	0.657													C|||	525	0.104832	0.1997	0.0461	5008	,	,		16955	0.128		0.0308	False		,,,				2504	0.0706				p.R292S		Atlas-SNP	.											PPARGC1B,NS,carcinoma,0,1	PPARGC1B	74	1	0			c.C874A						PASS	.	C	SER/ARG,SER/ARG,SER/ARG	776,3630	307.5+/-290.0	63,650,1490	48.0	57.0	54.0		757,682,874	5.8	1.0	5	dbSNP_120	54	292,8308	106.0+/-166.9	5,282,4013	yes	missense,missense,missense	PPARGC1B	NM_001172698.1,NM_001172699.1,NM_133263.3	110,110,110	68,932,5503	AA,AC,CC		3.3953,17.6123,8.2116	probably-damaging,probably-damaging,probably-damaging	253/985,228/960,292/1024	149212510	1068,11938	2203	4300	6503	SO:0001583	missense	133522	exon5			CTCATACGCTACA	AF468496	CCDS4298.1, CCDS54933.1, CCDS54934.1	5q33.1	2013-02-12	2006-10-17		ENSG00000155846	ENSG00000155846		"""RNA binding motif (RRM) containing"""	30022	protein-coding gene	gene with protein product		608886	"""peroxisome proliferative activated receptor, gamma, coactivator 1, beta"""			11793024, 11854298	Standard	NM_133263		Approved	PERC, PGC1B	uc003lrc.3	Q86YN6	OTTHUMG00000130055	ENST00000309241.5:c.874C>A	5.37:g.149212510C>A	ENSP00000312649:p.Arg292Ser	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	89	6	0.0674157	NM_133263	A2RUM8|A2RUN0|B3KVW0|Q86YN3|Q86YN4|Q86YN5|Q8N1N9|Q8TDE4|Q8TDE5	Missense_Mutation	SNP	ENST00000309241.5	37	CCDS4298.1	196	0.08974358974358974	89	0.18089430894308944	16	0.04419889502762431	66	0.11538461538461539	25	0.032981530343007916	C	20.6	4.011421	0.75046	0.176123	0.033953	ENSG00000155846	ENST00000360453;ENST00000394320;ENST00000309241;ENST00000403750	T;T;T;T	0.12465	2.69;2.78;2.79;2.68	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	T	0.00073	0.0002	M	0.61703	1.905	0.26653	P	0.9720632	D;D;D;D;D	0.76494	0.999;0.994;0.999;0.999;0.998	D;P;D;P;D	0.67382	0.951;0.879;0.951;0.894;0.95	T	0.00004	-1.2558	9	0.56958	D	0.05	-22.9034	19.976	0.97309	0.0:1.0:0.0:0.0	rs11959820;rs52793886;rs58815357;rs11959820	271;271;253;292;292	Q86YN6-2;Q86YN6-4;Q86YN6-5;Q86YN6;Q86YN6-3	.;.;.;PRGC2_HUMAN;.	S	253;292;292;228	ENSP00000353638:R253S;ENSP00000377855:R292S;ENSP00000312649:R292S;ENSP00000384403:R228S	ENSP00000312649:R292S	R	+	1	0	PPARGC1B	149192703	1.000000	0.71417	0.986000	0.45419	0.947000	0.59692	4.437000	0.59955	2.713000	0.92767	0.655000	0.94253	CGC	C|0.912;A|0.087	0.087	strong		0.657	PPARGC1B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252334.1	NM_133263	
